http://wiki.docking.org/api.php?action=feedcontributions&feedformat=atom&user=FrodoDISI - User contributions [en]2026-10-12T21:35:16ZUser contributionsMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Category:Captcha&diff=17651Category:Captcha2026-10-07T19:20:01Z<p>Frodo: asdf</p>
<hr />
<div>We use captcha for <br />
* ZINC15<br />
* ZINC20<br />
* ZINC22<br />
* ZINC26<br />
* and maybe SEA and maybe some other services. <br />
<br />
This is because we keep getting hit by bots that crash our servers. I wish there was another way. This is the only way we have found to survive.</div>Frodohttp://wiki.docking.org/index.php?title=ZINC20:Command_line_with_captcha&diff=17650ZINC20:Command line with captcha2026-10-07T19:18:55Z<p>Frodo: asdf</p>
<hr />
<div>You must get the session cookie from your browser first.<br />
* Step 1 - Solve captcha in browser<br />
<br />
* Step 2 - Extract the session cookie<br />
Open browser DevTools -> Application tab -> Cookies -> find the session cookie. Copy the session value.<br />
<br />
* Step 3 - Use it with curl<br />
curl -b "session=..." "https://zinc.docking.org/substances/subsets/fda.csv?count=all" -o fda.csv<br />
With wget<br />
wget --header="Cookie: session=..." "https://zinc.docking.org/substances/subsets/fda.txt?count=all" -O fda.txt<br />
<br />
It is a bit messy, but it works. <br />
<br />
Captcha is necessary because we keep getting hit by bots. I do hope the bots are not clever enough to use this wiki page to engineer a solution that gets around the captcha. Who am I kidding? <br />
<br />
[[Category:ZINC]]<br />
[[Category:ZINC15]]<br />
[[Category:ZINC20]]<br />
[[Category:Captcha]]</div>Frodohttp://wiki.docking.org/index.php?title=Category:CoreHPC&diff=17647Category:CoreHPC2026-10-02T20:25:36Z<p>Frodo: asdf</p>
<hr />
<div>This is the category tag for coreHPC, our new shared cluster in Santa Clara. <br />
<br />
All procedures and protocols that are specific to CoreHPC should be tagged with this Category so that they are all grouped together.</div>Frodohttp://wiki.docking.org/index.php?title=Transition_to_coreHPC&diff=17646Transition to coreHPC2026-10-02T20:24:42Z<p>Frodo: /* Please write things down */ asdf</p>
<hr />
<div>This is about the transition to [[Cluster 8]] also known as CoreHPC / Santa Clara. <br />
<br />
* There is a web page: https://ars.ucsf.edu/wynton-transition-keeping-you-informed<br />
<br />
== Timeline ==<br />
* We can get accounts on CoreHPC NOW - Sept 2026. Please get one if you want to do LSD after Feb 1, 2027. We can help you if you have any trouble. Our FAC number is CX900007_DS1.<br />
* Wynton will be shutting down in Spring 2027. Anything you leave on Wynton after Feb 1, 2027 is potentially at risk. We will try to help, but you are responsible for your own projects and your own data. <br />
* Database building and docking is working on CoreHPC! Thank you to Katie! Instructions here: [[Building and Docking on CoreHPC]].<br />
* Katie is currently porting ChemSTEP<br />
* If you port something, please a. write a wiki page. b. tell others. c. have someone test your protocol. d. tell me it is "ready". Thank you. <br />
* I am actively recruiting volunteers to help port other parts of our software. Thank you. <br />
<br />
== What you should do NOW if you are a Wynton user or you need more compute than we have locally on C2 and C7 ==<br />
* Start reducing your footprint on Wynton aka [[Cluster 3]]. <br />
* For projects that are finished (published, abandoned) or small, please: <br />
** gzip/delete/tar aggressively, writing READMEs in each major directory for anyone who might use them in future<br />
** move data off Wynton to C7. We recommend against C2, because we are trying to reduce it. But C2 is better than not at all.<br />
** make a separate backup using an external USB disk. These are available in my office BH508A.<br />
** make a copy of your backup (you get one, we keep one), doubling the chances that the file can be recovered one day. We can help. <br />
** label the disk, and write an email or wiki page about it, so we know what it is. <br />
** when you are sure it is backed up. delete from Wynton. As our footprint is reduced, it will become easier to see what is left. <br />
* For projects that are ongoing: <br />
** be aware that you have about 5 months left, so it is not too soon to start backing up critical files. <br />
** if you do not really need Wynton, and could run on C7 or C8 (coreHPC), consider transitioning now to save trouble later. <br />
** look critically at the files you control on Wynton and delete whatever you can if safe. e.g. temporary files. things you tried, and don't care about any more. <br />
<br />
== What's next ==<br />
* we will start really hassling you about moving to [[Cluster 8]] aka CoreHPC in January 2027. You don't want to be hassled, get started now.<br />
* I will remind you about this every week from now until Feb 1, 2026. <br />
<br />
== Please write things down == <br />
* Please write a wiki page for any new procedure you develop on C7 or C8.<br />
* Please write a wiki page for any backup you make that you deposit with us. <br />
* You can write a wiki page, e.g. "My move to CoreHPC, volume 1" to track your progress. This is going to be complicated, best to communicate what you are doing. Tag your pages with [[Category:Transition 2027]].<br />
<br />
Thank you<br />
<br />
[[Category:Cluster]]<br />
[[Category:Transition 2027]]<br />
[[Category:coreHPC]]</div>Frodohttp://wiki.docking.org/index.php?title=Running_ChemSTEP_on_CoreHPC&diff=17645Running ChemSTEP on CoreHPC2026-10-02T20:24:38Z<p>Frodo: /* 9. Monitor Job Status */ asdf</p>
<hr />
<div>== 1. Source Environment ==<br />
<br />
<pre><br />
source /mnt/fac/CX900007_DS1/soft/chemstep/env.sh<br />
</pre><br />
<br />
== 2. Dock the Seed Set ==<br />
<br />
Copy the <code>.sdi</code> file for the library you want to use into a directory containing your dockfiles:<br />
<br />
{| class="wikitable"<br />
! Library !! Path<br />
|-<br />
| 22B || <code>cp -r /mnt/fac/CX900007_DS1/work/kholland/22B_seed_building/sdi ./sdi</code><br />
|}<br />
<br />
Then dock the seed set:<br />
<pre><br />
bash /mnt/fac/CX900007_DS1/soft/super_dock3r.sh<br />
</pre><br />
<br />
== 3. Gather Scores for the Seed Set ==<br />
<br />
Once docking is complete, run the following from the directory '''one level above''' your docking output (<code>MOLECULES_DIR_TO_BIND</code>).<br />
<br />
'''22B library:'''<br />
<pre><br />
python python $CHEMSTEP_INSTALL_PATH/chemstep-development/accessory/get_scores.py 0<br />
</pre><br />
<br />
<br />
Verify that <code>scores_round_0.txt</code> was correctly written:<br />
<pre><br />
wc -l scores_round_0.txt<br />
</pre><br />
<br />
== 4. Convert Scores to .npy Files ==<br />
<br />
Convert scores to ChemSTEP-readable <code>.npy</code> files:<br />
<br />
<pre><br />
python $CHEMSTEP_INSTALL_PATH/chemstep-development/accessory/convert_scores_to_npy.py 0 CSLB<br />
</pre><br />
<br />
<br />
== 5. Set Up the ChemSTEP Run Directory ==<br />
<br />
Create and enter a new run directory, then copy in the necessary files:<br />
<br />
<pre><br />
mkdir chemstep_run<br />
cd chemstep_run<br />
chemstep-run-new<br />
</pre><br />
<br />
This will populate the directory with <code>params.txt</code>, <code>run_chemstep.py</code>, and <code>launch_chemstep_as_job.sh</code>.<br />
<br />
=== Optional: Integrated IFP ===<br />
<br />
If running with integrated IFP for beacon selection, also run:<br />
<br />
<pre><br />
chemstep-run-ifp<br />
</pre><br />
<br />
This copies in the additional files <code>ifp_acceptance_criteria.txt</code> and <code>interactions.txt</code>.<br />
<br />
== 6. Edit params.txt ==<br />
<br />
Add the absolute paths to the ChemSTEP-readable score and indices <code>.npy</code> arrays generated in Step 4.<br />
<br />
<pre><br />
seed_indices_file: /path/to/your/indices_round_0.npy<br />
seed_scores_file: /path/to/your/scores_round_0.npy<br />
hit_pprop: 5.5<br />
n_docked_per_round: 2000000<br />
bundle_size: 1000<br />
max_beacons: 100<br />
max_n_rounds: 250<br />
</pre><br />
<br />
=== Parameter Reference ===<br />
<br />
{| class="wikitable"<br />
! Parameter !! Description<br />
|-<br />
| <code>hit_pprop</code> || Defines a "virtual hit." pProp = −log(rank%) within the total library score distribution. E.g., pProp 4 in 13B space ≈ top 0.01% (~1.3M molecules); pProp 5 ≈ 0.001% (~132K). The seed set should contain at least 10<sup>(pProp+2)</sup> molecules.<br />
|-<br />
| <code>n_docked_per_round</code> || Number of molecules prioritized per round. All must be built and docked between rounds. Too many slows throughput and may reduce diversity; too few slows virtual hit recovery. Recommended: 1-2 million<br />
|-<br />
| <code>max_beacons</code> || Diverse, well-scoring molecules used to guide prioritization. All molecules above the pProp threshold are candidates. Too many reduce inter-beacon diversity; too few hinder space exploration. Fewer beacons than specified may be assigned if an insufficient number of molecules clear the threshold. Recommended: 100 <br />
|-<br />
| <code>bundle_size</code> || In auto docking mode, number of molecules submitted as a single build job.<br />
|-<br />
| <code>max_n_rounds</code> || No adjustment needed when running ChemSTEP prospectively as described here.<br />
|}<br />
<br />
== 7. Edit run_chemstep.py ==<br />
<br />
'''Note:''' All paths must be '''absolute paths'''.<br />
<br />
=== Required Settings ===<br />
<br />
Set <code>lib_path</code> to the library pickle for your library:<br />
<br />
{| class="wikitable"<br />
! Library !! Path<br />
|-<br />
| 22B || <code>/mnt/fac/CX900007_DS1/work/kholland/22B_fp_lib/22B_fplib.pickle</code><br />
|}<br />
<br />
<pre><br />
lib_path = '/full/path/to/library.pickle'<br />
</pre><br />
<br />
Set <code>dockfiles_path</code>:<br />
<br />
<pre><br />
dockfiles_path="/full/path/to/dockfiles"<br />
</pre><br />
<br />
=== Optional: minTD Exclusion Zone ===<br />
<br />
Molecules will not be prioritized from within a specified Tanimoto distance of beacons. Comment in the relevant lines and update the value. Consider also setting <code>enforce_n_docked_per_round = True</code> when using this option:<br />
<br />
<pre><br />
min_td_search=0.5,<br />
enforce_n_docked_per_round=True,<br />
</pre><br />
<br />
=== Optional: Integrated IFP ===<br />
<br />
Only selects beacons that satisfy user-defined interaction criteria. Comment in the following lines and update the paths to the necessary files (copied in Step 5 if you ran <code>chemstep-run-ifp</code>):<br />
<br />
<pre><br />
use_IFP=True,<br />
ifp_pdb_path='/full/path/to/rec.crg.pdb',<br />
interactions_file='/full/path/to/interactions.txt',<br />
ifp_acceptance_criteria_file='/full/path/to/ifp_acceptance_criteria.txt',<br />
</pre><br />
<br />
'''<code>interactions.txt</code>''' — one interaction per line, comma-separated. Format: <code>interaction_type, residue_name_and_number</code>. Example:<br />
<br />
<pre><br />
Hydrogen bond, GLY-19<br />
Ionic, ASP-149<br />
</pre><br />
<br />
Supported interaction types include: Proximal, Hydrogen bond, Ionic, Cation-pi, Hydrophobic, Halogen bond, and others. See LUNA and IFP documentation for the full list.<br />
<br />
'''<code>ifp_acceptance_criteria.txt</code>''' — defines the number of unsatisfied donors/acceptors/specific interactions required for a molecule to pass IFP and be considered for beacon selection. Example:<br />
<br />
<pre><br />
#_donors<br />
#_acceptors<br />
#_unstatisfied_donors == 0<br />
#_unstatisfied_acceptors <= 4<br />
Ionic/ASP-149 > 0<br />
</pre><br />
<br />
<br />
=== Optional: SMARTS exclusion filter ===<br />
Integrated SMARTS filer can exclude problematic chemotypes from being built, docked, or selected as beacons. Multiple SMARTS patterns are tolerated. Comment in the following line in run_chemstep.py: <br />
<br />
<pre><br />
filter_smarts=['n1cncnc1', 'c1cccnc1[SH]']<br />
</pre><br />
<br />
TRIAZINES: 'n1cncnc1'<br />
<br />
=== Example: AmpC on 22B with minTD=0.50, No IFP ===<br />
<br />
<pre><br />
lib_path = '/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/scripts/libraries/22B/22B_fplib.pickle'<br />
lib = load_library_from_pickle(lib_path)<br />
algo = CSAlgo(lib, 'params.txt', 'output', 16, verbose=True,<br />
scheduler='sge', smi_id_prefix='CSLB',<br />
python_exec="/wynton/group/bks/work/shared/kholland/chemstep_auto_v04/bin/python",<br />
dockfiles_path="/wynton/group/bks/work/kholland/chemstep_ampc_22B/seed_docking/dockfiles",<br />
min_td_search=0.5,<br />
enforce_n_docked_per_round=True,<br />
#use_IFP=True,<br />
#ifp_pdb_path='/path/to/your/reference/rec.crg.pdb',<br />
#interactions_file='/path/to/your/interactions.txt',<br />
#ifp_acceptance_criteria_file='/path/to/your/ifp_acceptance_criteria.txt',<br />
docking_method="auto", track_beacon_orig=True)<br />
</pre><br />
<br />
== 8. Launch the Job ==<br />
<br />
Submit the main ChemSTEP job:<br />
<br />
<pre><br />
sbatch launch_chemstep_as_job.sh<br />
</pre><br />
<br />
== 9. Monitor Job Status ==<br />
<br />
Check job status with <code>squeue -u USER_ID</code>. The main job will run for up to '''6 days''' given no errors. ChemSTEP will launch search, building, and docking jobs in successive rounds.<br />
<br />
'''Note:''' If any building or docking subjobs hang, the main job will not proceed until those are canceled or finished. Monitor job statuses regularly and occasionally verify that docking output files (<code>scores_round_*.txt</code>) are being populated.<br />
<br />
<br />
[[Category:coreHPC]]<br />
<br />
[[Category:Transition 2027]]<br />
[[Category:Cluster]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Synthons&diff=17637ZINC26:Catalogs:Synthons2026-10-02T17:42:15Z<p>Frodo: /* Synthons (Arthor) */ asdf</p>
<hr />
<div>== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Purchasable_Databases&diff=17636ZINC26:Purchasable Databases2026-10-02T17:41:47Z<p>Frodo: /* In-Stock Catalog detail */ asdf</p>
<hr />
<div><br />
This is all about purchasable databases.<br />
* Back to [[ZINC26]]<br />
* Back to [[ZINC26:Help]]<br />
<br />
== Purchasable == <br />
* inStock-1 - preferred sources for inStock screening compounds (SC)<br />
** chemspace<br />
** chembridge<br />
** enamine <br />
** mcule<br />
** molport<br />
** sial<br />
<br />
* inStock-2 - Other vendors<br />
** chemdiv<br />
** many many others<br />
<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
** Enamine M<br />
** Enamine S <br />
** OnePot<br />
** xtalPi<br />
** wuxi <br />
<br />
* onDemand-2 - Other SC onDemand<br />
** others<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]<br />
<br />
<br />
<br />
<br />
== Purchasable Catalogs in ZINC26 ==<br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules. <br />
|-<br />
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)<br />
|-<br />
| WuXi || GalaXi || 29B || must check || July 2026<br />
|-<br />
| OnePot || 20M || 20B || expecting update this week || comments<br />
|-<br />
| XtalPi || VAST || 20B || good || comments<br />
|-<br />
| Various || In Stock || 20M || needs updating || see table below<br />
|-<br />
| Various || Covalent || 20M || needs updating || see table below<br />
|-<br />
| Various || BB || 20M || needs updating || see table below<br />
|-<br />
| - || Total || 100B || <br />
|}<br />
<br />
<br />
== In-Stock Catalog detail ==<br />
<br />
We have 100s of vendors. <br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Various || In Stock || 20M || needs updating || see table below<br />
|-<br />
| Various || Covalent || 20M || needs updating || see table below<br />
|-<br />
| Various || BB || 20M || needs updating || see table below<br />
|-<br />
| - || Total || 100B || <br />
|}<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17635ZINC26:Help2026-10-02T17:41:20Z<p>Frodo: /* Database Organization */ aSD</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [[ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
{| class="wikitable"<br />
|-<br />
! Batch Category !! # files !! size !! Catalogs<br />
|-<br />
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi, <br />
|-<br />
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP<br />
|-<br />
|}<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
=== The API === <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17634ZINC26:Help2026-10-02T17:41:03Z<p>Frodo: /* Work in progress */ adsf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
{| class="wikitable"<br />
|-<br />
! Batch Category !! # files !! size !! Catalogs<br />
|-<br />
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi, <br />
|-<br />
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP<br />
|-<br />
|}<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
=== The API === <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17633ZINC26:Help2026-10-02T17:40:28Z<p>Frodo: /* Additional access with login */ asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
{| class="wikitable"<br />
|-<br />
! Batch Category !! # files !! size !! Catalogs<br />
|-<br />
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi, <br />
|-<br />
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP<br />
|-<br />
|}<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
=== The API === <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17632ZINC26:Help2026-10-02T17:39:37Z<p>Frodo: asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
{| class="wikitable"<br />
|-<br />
! Batch Category !! # files !! size !! Catalogs<br />
|-<br />
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi, <br />
|-<br />
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP<br />
|-<br />
|}<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
=== The API === <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17631ZINC26:Help2026-10-02T17:38:42Z<p>Frodo: asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
=== The API === <br />
Description here.<br />
<br />
== Catalogs included in Batch search ==<br />
<br />
{| class="wikitable"<br />
|-<br />
! Batch Category !! # files !! size !! Catalogs<br />
|-<br />
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi, <br />
|-<br />
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP<br />
|-<br />
|}<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17630ZINC26:Help2026-10-02T17:38:13Z<p>Frodo: /* How to use the Interface */ asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== Catalogs included in Batch search ==<br />
<br />
{| class="wikitable"<br />
|-<br />
! Batch Category !! # files !! size !! Catalogs<br />
|-<br />
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi, <br />
|-<br />
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP<br />
|-<br />
|}<br />
<br />
== The API == <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Databases&diff=17629ZINC26:Databases2026-10-02T17:37:36Z<p>Frodo: asdf</p>
<hr />
<div>Here are the databases currently included in ZINC26, as well as which are included in batch searches. <br />
<br />
== Purchasable Catalogs in ZINC26 ==<br />
[[ZINC26:Purchasable Databases]]<br />
<br />
[[ZINC26:Bioactive Databases]]<br />
<br />
<br />
== BB Catalog Detail == <br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Chem-Space|| In-Stock || 500K ||<br />
|-<br />
| MolPort || In-Stock || 2M ||<br />
|-<br />
| Enamine|| FastMADE || 120M || <br />
|-<br />
| Enamine || MADE | 1.35B || <br />
|-<br />
| - || Total || 100B || <br />
|}<br />
Question: how many BB are there that are not covered by the above: Molport+ChemSpace+MADE ? <br />
We don't know, but we will find out. <br />
<br />
== Covalent Catalog Detail == <br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Enamine || Covalent || 1B <br />
|-<br />
| - || Total || 1B || <br />
|}<br />
So far, Enamine is the only reliable covalent vendor. There are in stock and on demand compounds. <br />
Let's add any other covalent vendors here, but warhead. Maybe we can fish them out of commercially available compounds?<br />
<br />
<br />
[[Cluster_7:Libraries]]<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17628ZINC26:Help2026-10-02T17:37:07Z<p>Frodo: /* Database Organization */ asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Special Databases]]. do not fit elsewhere, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]] - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== The API == <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Special_Databases&diff=17627ZINC26:Special Databases2026-10-02T17:36:29Z<p>Frodo: asdf</p>
<hr />
<div>== Special Databases ==<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database, about 15,000 compounds. See advisor.docking.org<br />
* Covalent - purchasable covalent libraries<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]<br />
<br />
<br />
We have 100s of vendors. <br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Aggregators|| Aggregators || 13000 || needs updating || see table below<br />
|-<br />
| - || Total || 100B || <br />
|}<br />
<br />
<br />
Back to [[ZINC26:Help]]<br />
<br />
[[Category:Databases]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Special&diff=17626ZINC26:Catalogs:Special2026-10-02T17:36:10Z<p>Frodo: asdf</p>
<hr />
<div></div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17625ZINC26:Help2026-10-02T17:35:59Z<p>Frodo: /* Database Organization */ asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] - screening compounds you can buy<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]. * Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]]. * Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== The API == <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Purchasable_Databases&diff=17624ZINC26:Purchasable Databases2026-10-02T17:35:35Z<p>Frodo: asdf</p>
<hr />
<div><br />
This is all about purchasable databases.<br />
* Back to [[ZINC26]]<br />
* Back to [[ZINC26:Help]]<br />
<br />
== Purchasable == <br />
* inStock-1 - preferred sources for inStock screening compounds (SC)<br />
** chemspace<br />
** chembridge<br />
** enamine <br />
** mcule<br />
** molport<br />
** sial<br />
<br />
* inStock-2 - Other vendors<br />
** chemdiv<br />
** many many others<br />
<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
** Enamine M<br />
** Enamine S <br />
** OnePot<br />
** xtalPi<br />
** wuxi <br />
<br />
* onDemand-2 - Other SC onDemand<br />
** others<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]<br />
<br />
<br />
<br />
<br />
== Purchasable Catalogs in ZINC26 ==<br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules. <br />
|-<br />
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)<br />
|-<br />
| WuXi || GalaXi || 29B || must check || July 2026<br />
|-<br />
| OnePot || 20M || 20B || expecting update this week || comments<br />
|-<br />
| XtalPi || VAST || 20B || good || comments<br />
|-<br />
| Various || In Stock || 20M || needs updating || see table below<br />
|-<br />
| Various || Covalent || 20M || needs updating || see table below<br />
|-<br />
| Various || BB || 20M || needs updating || see table below<br />
|-<br />
| - || Total || 100B || <br />
|}<br />
<br />
<br />
== In-Stock Catalog detail ==<br />
<br />
We have 100s of vendors. <br />
<br />
{| class="wikitable"<br />
|-<br />
! Vendor !! Catalog !! size !! status !! Date<br />
|-<br />
| Various || In Stock || 20M || needs updating || see table below<br />
|-<br />
| Various || Covalent || 20M || needs updating || see table below<br />
|-<br />
| Various || BB || 20M || needs updating || see table below<br />
|-<br />
| - || Total || 100B || <br />
|}<br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Purchasable&diff=17623ZINC26:Catalogs:Purchasable2026-10-02T17:35:10Z<p>Frodo: asdf</p>
<hr />
<div></div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17622ZINC26:Help2026-10-02T17:34:55Z<p>Frodo: /* Database Organization */ sdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [ZINC26:Bioactive Databases]] - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] * [[ZINC26:Catalogs:Purchasable]] merge. * Purchasable - screening compounds you can buy<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]. * Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]]. * Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== The API == <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Bioactive_Databases&diff=17621ZINC26:Bioactive Databases2026-10-02T17:34:29Z<p>Frodo: asdf</p>
<hr />
<div>== Bioactive Databases in ZINC26 == <br />
<br />
== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36) <br />
* metabolites<br />
* natural<br />
* otherdrugs<br />
* various<br />
<br />
{| class="wikitable"<br />
|-<br />
! Category !! Catalog !! size !! date !! comments<br />
|-<br />
| inVitro || ChEMBL 36 1uM || 700K || July 2025 || other constraints apply<br />
|-<br />
| inVivo || DrugBank || 10K || March 2026 || update annually or better<br />
|-<br />
| Natural || Cocounut || 715K || May 2026 || update quarterly if possible<br />
|-<br />
| Natural || catalog2 || xx || xx || xx<br />
|-<br />
| Total || 1M ||<br />
|}<br />
<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Bioactive&diff=17620ZINC26:Catalogs:Bioactive2026-10-02T17:33:51Z<p>Frodo: asdf</p>
<hr />
<div></div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17619ZINC26:Help2026-10-02T17:33:14Z<p>Frodo: /* Database Organization */ adsf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* [[ZINC26:Catalogs:Bioactive]]. * * [[ZINC26:Bioactive Databases]] Bioactive - molecules with reported biological activity <br />
* [[ZINC26:Purchasable Databases]] * [[ZINC26:Catalogs:Purchasable]] merge. * Purchasable - screening compounds you can buy<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]. * Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* [[ZINC26:Catalogs:Synthons]]. * Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== The API == <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17618ZINC26:Help2026-10-02T17:32:17Z<p>Frodo: /* More notes */ asd</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
<br />
* [[ZINC26:Catalogs:Bioactive]]. * * [[ZINC26:Bioactive Databases]] merge<br />
* [[ZINC26:Purchasable Databases]] * [[ZINC26:Catalogs:Purchasable]] merge<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]<br />
* [[ZINC26:Catalogs:Synthons]]<br />
<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== The API == <br />
Description here.<br />
<br />
== Levels of Access and Limitations == <br />
<br />
* There are four levels of access. <br />
* anonymous users - no login required. One molecule at a time in batch.<br />
** All Smallworld databases are visibile, but only small Arthor databases are visible.<br />
<br />
* authenticated users - more privileges. Ten molecules at a time in batch.<br />
** All Arthor databases are visible, but there is a time limit on searches. <br />
<br />
* UCSF users - more access for folks in our research group.<br />
** Higher limits required for our own research and testing<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17617ZINC26:Help2026-10-02T17:28:30Z<p>Frodo: /* How to use the Interface */ asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
<br />
* [[ZINC26:Catalogs:Bioactive]]. * * [[ZINC26:Bioactive Databases]] merge<br />
* [[ZINC26:Purchasable Databases]] * [[ZINC26:Catalogs:Purchasable]] merge<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]<br />
* [[ZINC26:Catalogs:Synthons]]<br />
<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== The API == <br />
Description here.<br />
<br />
== More notes == <br />
<br />
* Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction. <br />
* You must complete a captcha each time you open a new window to protect us from bots. <br />
* We throttle usage in various ways that allow us to offer a free public service without overloading.<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17616ZINC26:Help2026-10-02T17:28:05Z<p>Frodo: asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
<br />
* [[ZINC26:Catalogs:Bioactive]]. * * [[ZINC26:Bioactive Databases]] merge<br />
* [[ZINC26:Purchasable Databases]] * [[ZINC26:Catalogs:Purchasable]] merge<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]<br />
* [[ZINC26:Catalogs:Synthons]]<br />
<br />
* [[ZINC26:Progress]]<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
== More notes == <br />
<br />
* Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction. <br />
* You must complete a captcha each time you open a new window to protect us from bots. <br />
* We throttle usage in various ways that allow us to offer a free public service without overloading.<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Help&diff=17615ZINC26:Help2026-10-02T17:26:59Z<p>Frodo: /* Current Contents and Status of Databases */ asdf</p>
<hr />
<div>ZINC26 is a search tool for purchasable and precedented bioactive chemical space. It uses [[Smallworld]] and [[Arthor]] technology from [[NextMove Software]] to allow billions of molecules to be searched in seconds. There are three ways to use ZINC26: Interactive, Batch, and an API.<br />
<br />
== How to use the Interface == <br />
<br />
=== Batch interface === <br />
ZINC26 batch allows you to search all purchasable molecules to find the most similar in a short transaction. The resulting zip file can be downloaded and opened with DataWarrior (openmolecules.org, free). A guide on using DataWarrior to navigate the results is available [[ZINC26:DataWarrior]].<br />
<br />
=== Interactive interface ===<br />
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly. The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each.<br />
<br />
[[ZINC26:Organization]]<br />
<br />
<br />
== Database Organization == <br />
In both the interactive and batch interfaces, the top level categories are:<br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* Synthons - reagents you can buy<br />
<br />
* [[ZINC26:Databases]]<br />
<br />
* [[ZINC26:Catalogs:Bioactive]]. * * [[ZINC26:Bioactive Databases]] merge<br />
* [[ZINC26:Purchasable Databases]] * [[ZINC26:Catalogs:Purchasable]] merge<br />
* [[ZINC26:Catalogs:Special]]. * [[ZINC26:Special Databases]]<br />
* [[ZINC26:Catalogs:Synthons]]<br />
<br />
* [[ZINC26:Progress]]<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]<br />
<br />
== More notes == <br />
<br />
* Anonymous users can search for one molecule at a time in the batch interface, while logged in users may search for up to 10 molecules in a single transaction. <br />
* You must complete a captcha each time you open a new window to protect us from bots. <br />
* We throttle usage in various ways that allow us to offer a free public service without overloading.<br />
<br />
== Questions I can ask == <br />
[[ZINC26:Questions]]<br />
<br />
== Updates / Status == <br />
* writing paper<br />
* checking everything<br />
* testing<br />
* we need to create/update the "All-" databases <br />
<br />
== Report Problems / Suggestions == <br />
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9<br />
* Send us catalogs that you do not see indexed.<br />
<br />
== Additional access with login == <br />
If you login, you get extra access. This includes:<br />
* being able to search 10 SMILES at a time in batch instead of 1. <br />
* access to Arthor<br />
* access to Synthons<br />
<br />
== Work in progress ==<br />
We are still assembling various "all-" type databases. They will appear soon, and will provide the ability to search all molecules to some heavy atom count in a single interactive search. <br />
<br />
<br />
<br />
[[Category:ZINC26]]<br />
[[Category:JJI]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17614ZINC26:Organization2026-10-02T17:23:52Z<p>Frodo: asdf</p>
<hr />
<div></div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Special&diff=17613ZINC26:Catalogs:Special2026-10-02T17:22:47Z<p>Frodo: asdf</p>
<hr />
<div>== Special == <br />
* Aggregators - so far only one "special" database, about 15,000 compounds. See advisor.docking.org<br />
* Covalent - purchasable covalent libraries<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17612ZINC26:Organization2026-10-02T17:22:11Z<p>Frodo: asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories, includes covalent, chemistry commons.<br />
* Synthons - reagents you can buy<br />
<br />
Dedicated pages keep track of the details of each area:<br />
<br />
== Bioactive ==<br />
[[ZINC26:Catalogs:Bioactive]]<br />
<br />
[[ZINC26:Catalogs:Purchasable]]<br />
<br />
[[ZINC26:Catalogs:Special]]<br />
<br />
[[ZINC26:Catalogs:Synthons]]<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Synthons&diff=17611ZINC26:Catalogs:Synthons2026-10-02T17:20:01Z<p>Frodo: asdf</p>
<hr />
<div>== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17610ZINC26:Organization2026-10-02T17:19:32Z<p>Frodo: asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
The detailed breakdown of each of these is below. <br />
<br />
<br />
== Bioactive ==<br />
[[ZINC26:Catalogs:Bioactive]]<br />
<br />
[[ZINC26:Catalogs:Purchasable]]<br />
<br />
[[ZINC26:Catalogs:Special]]<br />
<br />
[[ZINC26:Catalogs:Synthons]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Special&diff=17609ZINC26:Catalogs:Special2026-10-02T17:18:32Z<p>Frodo: asdf</p>
<hr />
<div>== Special == <br />
* Aggregators - so far only one "special" database, about 15,000 compounds. See advisor.docking.org<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17608ZINC26:Organization2026-10-02T17:18:04Z<p>Frodo: /* Bioactive */ asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
The detailed breakdown of each of these is below. <br />
<br />
<br />
== Bioactive ==<br />
[[ZINC26:Catalogs:Bioactive]]<br />
<br />
[[ZINC26:Catalogs:Purchasable]]<br />
<br />
[[ZINC26:Catalogs:Special]]<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17607ZINC26:Organization2026-10-02T17:17:48Z<p>Frodo: /* Special */ asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
The detailed breakdown of each of these is below. <br />
<br />
<br />
== Bioactive ==<br />
[[ZINC26:Catalogs:Bioactive]]<br />
<br />
[[ZINC26:Catalogs:Purchasable]]<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Purchasable&diff=17606ZINC26:Catalogs:Purchasable2026-10-02T17:17:20Z<p>Frodo: asdf</p>
<hr />
<div>== Purchasable == <br />
* inStock-1 - preferred sources for inStock screening compounds (SC)<br />
** chemspace<br />
** chembridge<br />
** enamine <br />
** mcule<br />
** molport<br />
** sial<br />
<br />
* inStock-2 - Other vendors<br />
** chemdiv<br />
** many many others<br />
<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
** Enamine M<br />
** Enamine S <br />
** OnePot<br />
** xtalPi<br />
** wuxi <br />
<br />
* onDemand-2 - Other SC onDemand<br />
** others<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
<br />
Back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17605ZINC26:Organization2026-10-02T17:16:32Z<p>Frodo: asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
The detailed breakdown of each of these is below. <br />
<br />
<br />
== Bioactive ==<br />
[[ZINC26:Catalogs:Bioactive]]<br />
<br />
[[ZINC26:Catalogs:Purchasable]]<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database, about 15,000 compounds. See advisor.docking.org<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Catalogs:Bioactive&diff=17604ZINC26:Catalogs:Bioactive2026-10-02T17:15:09Z<p>Frodo: asdf</p>
<hr />
<div>== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36) <br />
* metabolites<br />
* natural<br />
* otherdrugs<br />
* various<br />
<br />
back to [[ZINC26:Organization]]<br />
[[Category:ZINC26]]<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17595ZINC26:Organization2026-09-29T22:59:50Z<p>Frodo: /* Bioactive */ asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
The detailed breakdown of each of these is below. <br />
<br />
== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36) <br />
* metabolites<br />
* natural<br />
* otherdrugs<br />
* various<br />
<br />
== Purchasable == <br />
* inStock-1 - preferred sources for inStock screening compounds (SC)<br />
** chemspace<br />
** chembridge<br />
** enamine <br />
** mcule<br />
** molport<br />
** sial<br />
<br />
* inStock-2 - Other vendors<br />
** chemdiv<br />
** many many others<br />
<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
** Enamine M<br />
** Enamine S <br />
** OnePot<br />
** xtalPi<br />
** wuxi <br />
<br />
* onDemand-2 - Other SC onDemand<br />
** others<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database, about 15,000 compounds. See advisor.docking.org<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17594ZINC26:Organization2026-09-29T19:35:59Z<p>Frodo: asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are four top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
The detailed breakdown of each of these is below. <br />
<br />
== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36)<br />
* natural<br />
* metabolites<br />
* otherdrugs<br />
* other<br />
<br />
== Purchasable == <br />
* inStock-1 - preferred sources for inStock screening compounds (SC)<br />
** chemspace<br />
** chembridge<br />
** enamine <br />
** mcule<br />
** molport<br />
** sial<br />
<br />
* inStock-2 - Other vendors<br />
** chemdiv<br />
** many many others<br />
<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
** Enamine M<br />
** Enamine S <br />
** OnePot<br />
** xtalPi<br />
** wuxi <br />
<br />
* onDemand-2 - Other SC onDemand<br />
** others<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database, about 15,000 compounds. See advisor.docking.org<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock-1<br />
** Chembridge BB<br />
** Molport BB<br />
** ChemSpace BB<br />
** Enamine BB<br />
<br />
* inStock-2<br />
**<br />
**<br />
**<br />
<br />
* onDemand<br />
** FastMADE 120M<br />
** MADE 1.9 B<br />
** MADE_2h - deuterium enriched. 85K<br />
<br />
== Synthons (Arthor) == <br />
* by_price category: USD: 50, 100, 250, 500, 1000, fastMADE, MADE<br />
* by_role: functional group, role in Chemistry commons<br />
* by_name: by name.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17593ZINC26:Organization2026-09-29T17:29:45Z<p>Frodo: asd</p>
<hr />
<div>In interactive mode (magnifying glass) there are three top levels into which all databases are organized. <br />
<br />
* Bioactive - molecules with reported biological activity <br />
* Purchasable - screening compounds you can buy<br />
* Special - do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
== Purchasable == <br />
* inStock-1 - our preferred sources for inStock screening compounds (SC)<br />
** chemspace<br />
** chembridge<br />
** enamine <br />
** mcule<br />
** molport<br />
** sial<br />
<br />
* inStock-2 - Other SC in stock<br />
** chemdiv<br />
** many many others<br />
<br />
* macrocycles - purchasable macrocycles<br />
** Sept 2026 - 200M - peptidic - Enamine<br />
<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
** Enamine M<br />
** Enamine S <br />
** OnePot<br />
** xtalPi<br />
** wuxi <br />
<br />
* onDemand-2 - Other SC onDemand<br />
** others<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
<br />
=== Macrocycles === <br />
<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36)<br />
* natural<br />
* metabolites<br />
* otherdrugs<br />
* other<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database.<br />
* Frontier - new libraries from Enamine and others<br />
* Hartwig - current research<br />
* Ellman - current research<br />
* Commons - chemistry commons<br />
== Synthons (Smallworld) ==<br />
* inStock<br />
* onDemand<br />
<br />
== Synthons (Arthor) == <br />
* by_price<br />
* by_role<br />
* by_name<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17592ZINC26:Organization2026-09-29T17:17:08Z<p>Frodo: /* Purchasable */ adsf</p>
<hr />
<div>In interactive mode (magnifying glass) there are three top levels into which all databases are organized. <br />
* Purchasable - molecules you can buy<br />
* Bioactive - molecules with reported biological activity <br />
* Special - things that do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
<br />
== Purchasable == <br />
* inStock-1 - our preferred sources for inStock screening compounds (SC)<br />
* inStock-2 - Other SC in stock<br />
* macrocycles - purchasable macrocycles<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
* onDemand-2 - Other SC onDemand<br />
* zCommons - molecules we figure you can make from commercially available building blocks (Synthons)<br />
<br />
=== inStock-1 === <br />
<br />
<br />
=== inStock-2 ===<br />
<br />
<br />
=== Macrocycles === <br />
<br />
<br />
=== onDemand-1 ===<br />
<br />
=== onDemand-2 ===<br />
<br />
== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36)<br />
* metabolites<br />
* otherdrugs<br />
* other<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database.<br />
* Frontier - new libraries from Enamine and others<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock<br />
* onDemand<br />
<br />
== Synthons (Arthor) == <br />
* by_price<br />
* by_role<br />
* by_name<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17591ZINC26:Organization2026-09-29T17:16:39Z<p>Frodo: asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are three top levels into which all databases are organized. <br />
* Purchasable - molecules you can buy<br />
* Bioactive - molecules with reported biological activity <br />
* Special - things that do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
<br />
== Purchasable == <br />
* inStock-1 - our preferred sources for inStock screening compounds (SC)<br />
* inStock-2 - Other SC in stock<br />
* macrocycles - purchasable macrocycles<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
* onDemand-2 - Other SC onDemand<br />
* zCommons - molecules we figure you can make from commercially available building blocks (Synthons)<br />
<br />
=== Purchasable/inStock-1 === <br />
<br />
<br />
=== Purchasable/inStock-2 ===<br />
<br />
<br />
=== Purchasable/Macrocycles === <br />
<br />
<br />
=== Purchasable/onDemand-1 ===<br />
<br />
=== Purchasable/onDemand-2 ===<br />
<br />
== Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36)<br />
* metabolites<br />
* otherdrugs<br />
* other<br />
<br />
== Special == <br />
* Aggregators - so far only one "special" database.<br />
* Frontier - new libraries from Enamine and others<br />
<br />
== Synthons (Smallworld) ==<br />
* inStock<br />
* onDemand<br />
<br />
== Synthons (Arthor) == <br />
* by_price<br />
* by_role<br />
* by_name<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17590ZINC26:Organization2026-09-29T17:04:03Z<p>Frodo: /* Organization within Purchasable */ asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are three top levels into which all databases are organized. <br />
* Purchasable - molecules you can buy<br />
* Bioactive - molecules with reported biological activity <br />
* Special - things that do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
<br />
== Organization within Purchasable == <br />
* inStock-1 - our preferred sources for inStock screening compounds (SC)<br />
* inStock-2 - Other SC in stock<br />
* macrocycles - purchasable macrocycles<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
* onDemand-2 - Other SC onDemand<br />
* synthons - reagents you can buy<br />
* zCommons - molecules we figure you can make from commercially available building blocks (Synthons)<br />
<br />
=== Detail within Purchasable/inStock-1 === <br />
<br />
<br />
=== Detail within Purchasable/inStock-2 ===<br />
<br />
<br />
=== Detail within Purchasable/Macrocycles === <br />
<br />
<br />
=== Detail within Purchasable/onDemand-1 ===<br />
<br />
=== Detail within Purchasable/onDemand-2 ===<br />
<br />
== Organization within Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36)<br />
* metabolites<br />
* otherdrugs<br />
* other<br />
<br />
== Organization within Special == <br />
* Aggregators - so far only one "special" database.<br />
<br />
== Organization within Synthons in Smallworld ==<br />
* inStock<br />
* onDemand<br />
<br />
== Organization within Synthons in Arthor == <br />
* by_price<br />
* by_role<br />
* by_name<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=Category:Transition_2027&diff=17589Category:Transition 20272026-09-28T20:23:55Z<p>Frodo: asdf</p>
<hr />
<div>This is the cluster tag for the Transition of 2027 in which Wynton is closed and we start using coreHPC.<br />
<br />
* https://ars.ucsf.edu/wynton-transition-keeping-you-informed</div>Frodohttp://wiki.docking.org/index.php?title=Transition_to_coreHPC&diff=17588Transition to coreHPC2026-09-28T20:23:26Z<p>Frodo: asdf</p>
<hr />
<div>This is about the transition to [[Cluster 8]] also known as CoreHPC / Santa Clara. <br />
<br />
* There is a web page: https://ars.ucsf.edu/wynton-transition-keeping-you-informed<br />
<br />
== Timeline ==<br />
* We can get accounts on CoreHPC NOW - Sept 2026. Please get one if you want to do LSD after Feb 1, 2027. We can help you if you have any trouble. Our FAC number is CX900007_DS1.<br />
* Wynton will be shutting down in Spring 2027. Anything you leave on Wynton after Feb 1, 2027 is potentially at risk. We will try to help, but you are responsible for your own projects and your own data. <br />
* Database building and docking is working on CoreHPC! Thank you to Katie! Instructions here: [[Building and Docking on CoreHPC]].<br />
* Katie is currently porting ChemSTEP<br />
* If you port something, please a. write a wiki page. b. tell others. c. have someone test your protocol. d. tell me it is "ready". Thank you. <br />
* I am actively recruiting volunteers to help port other parts of our software. Thank you. <br />
<br />
== What you should do NOW if you are a Wynton user or you need more compute than we have locally on C2 and C7 ==<br />
* Start reducing your footprint on Wynton aka [[Cluster 3]]. <br />
* For projects that are finished (published, abandoned) or small, please: <br />
** gzip/delete/tar aggressively, writing READMEs in each major directory for anyone who might use them in future<br />
** move data off Wynton to C7. We recommend against C2, because we are trying to reduce it. But C2 is better than not at all.<br />
** make a separate backup using an external USB disk. These are available in my office BH508A.<br />
** make a copy of your backup (you get one, we keep one), doubling the chances that the file can be recovered one day. We can help. <br />
** label the disk, and write an email or wiki page about it, so we know what it is. <br />
** when you are sure it is backed up. delete from Wynton. As our footprint is reduced, it will become easier to see what is left. <br />
* For projects that are ongoing: <br />
** be aware that you have about 5 months left, so it is not too soon to start backing up critical files. <br />
** if you do not really need Wynton, and could run on C7 or C8 (coreHPC), consider transitioning now to save trouble later. <br />
** look critically at the files you control on Wynton and delete whatever you can if safe. e.g. temporary files. things you tried, and don't care about any more. <br />
<br />
== What's next ==<br />
* we will start really hassling you about moving to [[Cluster 8]] aka CoreHPC in January 2027. You don't want to be hassled, get started now.<br />
* I will remind you about this every week from now until Feb 1, 2026. <br />
<br />
== Please write things down == <br />
* Please write a wiki page for any new procedure you develop on C7 or C8.<br />
* Please write a wiki page for any backup you make that you deposit with us. <br />
* You can write a wiki page, e.g. "My move to CoreHPC, volume 1" to track your progress. This is going to be complicated, best to communicate what you are doing. Tag your pages with [[Category:Transition 2027]].<br />
<br />
Thank you<br />
<br />
[[Category:Cluster]]<br />
[[Category:Transition 2027]]</div>Frodohttp://wiki.docking.org/index.php?title=ZINC26:Organization&diff=17576ZINC26:Organization2026-09-25T20:17:58Z<p>Frodo: /* Organization */ asdf</p>
<hr />
<div>In interactive mode (magnifying glass) there are three top levels into which all databases are organized. <br />
* Purchasable - molecules you can buy<br />
* Bioactive - molecules with reported biological activity <br />
* Special - things that do not fit in other categories<br />
* Synthons - reagents you can buy<br />
<br />
<br />
== Organization within Purchasable == <br />
* inStock-1 - our preferred sources for inStock screening compounds (SC)<br />
* inStock-2 - Other SC in stock<br />
* macrocycles - purchasable macrocycles<br />
* onDemand-1 - our preferred sources for onDemand SC<br />
* onDemand-2 - Other SC onDemand<br />
* synthons - reagents you can buy<br />
* zCommons - molecules we figure you can make from commercially available building blocks (Synthons)<br />
<br />
=== Detail within Purchasable/inStock-1 === <br />
<br />
<br />
=== Detail within Purchasable/inStock-2 ===<br />
<br />
<br />
=== Detail within Purchasable/Macrocycles === <br />
<br />
<br />
=== Detail within Purchasable/onDemand-1 === <br />
<br />
== Organization within Bioactive ==<br />
* drugbank<br />
* food<br />
* hmdb<br />
* inVitro-01uM (ChEMBL36)<br />
* inVitro-03uM (ChEMBL36)<br />
* inVitro-10uM (ChEMBL36)<br />
* inVitro-30uM (ChEMBL36)<br />
* metabolites<br />
* otherdrugs<br />
* other<br />
<br />
== Organization within Special == <br />
* Aggregators - so far only one "special" database.<br />
<br />
== Organization within Synthons in Smallworld ==<br />
* inStock<br />
* onDemand<br />
<br />
== Organization within Synthons in Arthor == <br />
* by_price<br />
* by_role<br />
* by_name<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
** commons - chemistry commons<br />
** covalent - covalent<br />
** inStock<br />
** onDemand<br />
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)<br />
<br />
Back to [[ZINC26:Help]]<br />
[[Category:ZINC26]]</div>Frodohttp://wiki.docking.org/index.php?title=Category:ZINC26&diff=17575Category:ZINC262026-09-25T19:59:43Z<p>Frodo: asdf</p>
<hr />
<div>This is the main topic page for ZINC26, a database of molecules you can search and download created in 2026. <br />
<br />
Each article handles a separate subject, and all pages link back here to to the main [[ZINC26:Help]] page. <br />
<br />
If you are new to ZINC26, we suggest you start with [[ZINC26:Help]]. If you want to know more about the contents of ZINC26, check out [[ZINC26:Databases]]. To see examples of the sorts of questions you can ask, please look at [[ZINC26:Questions]]. To know what is still in progress, please see [[ZINC26:Progress]]. To learn about how databases are organized in ZINC26, please see [[ZINC26:Organization]]. <br />
<br />
Thank you for your interest. <br />
<br />
<br />
[[Category:Databases]]</div>Frodohttp://wiki.docking.org/index.php?title=Category:ZINC26&diff=17574Category:ZINC262026-09-25T19:59:08Z<p>Frodo: asdf</p>
<hr />
<div>This is the main topic page for ZINC26, a database of molecules you can search and download created in 2026. <br />
<br />
Each article handles a separate subject, and all pages link back here to to the main [[ZINC26:Help]] page. <br />
<br />
If you are new to ZINC26, we suggest you start with [[ZINC26:Help]]. If you want to know more about the contents of ZINC26, check out [[ZINC26:Databases]]. To see examples of the sorts of questions you can ask, please look at [[ZINC26:Questions]]. To know what is still in progress, please see [[ZINC26:Progress]]. <br />
<br />
Thank you for your interest. <br />
<br />
<br />
[[Category:Databases]]</div>Frodo