DISI - User contributions [en]

Cluster 8

2026-08-11T17:49:28Z

Frodo: /* how to do remote mounts */ asdf

We are still learning about FAC/coreHPC.

you will need to get separate (?) FAC and coreHPC accounts.
* FAC is for storage
* coreHPC is for compute
* it is more complicated than that, but it is a reasonable simplification.

* We collectively refer to FAC/coreHPC as "Cluster 8".
* We are attempting two strategies for cluster 8:
** upload ZINC on the fly, dock it, and then throw it away.
** nfs mount our cluster on coreHPC, data gets pulled as needed

* ZINC thus lives on our cluster (currently hosted on cluster 2, cross mounted read only to cluster 7).
* a copy of 50% of ZINC lives on Wynton/cluster 3.
* The pipe to FAC is 100 Gbps. Assming we get 50% of that, allows 1 TB in 3 minutes, and 3 PB is 6 days.
* thus, ftp/dock/delete.

* to get to corehpc
ssh <user>@chpc-ucsf-bastion-vm1.corehpc.ucsf.edu

* to get to slurm head node
ssh chpc-ucsf-login-vm1

* disks are
/mnt/scratch/user/<user>.
/mnt/home/<user>
/home/remote/<user> ; you land here when you login

== Learn more ==
https://wiki.library.ucsf.edu/spaces/CHPC/pages/720396955/CoreHPC+Access+Primer
https://it.ucsf.edu/service/corehpc
https://wiki.library.ucsf.edu/spaces/CHPC/pages/736476672/CoreHPC+Submission+Examples
https://wiki.library.ucsf.edu/spaces/CHPC/pages/751928275/CoreHPC+Technical+Overview

Anyone who uses coreHPC, please take notes, update this and other pages, and teach the rest of the lab how to use it. Thank you.

== how to do remote mounts ==
https://wiki.library.ucsf.edu/spaces/CHPC/pages/720396955/CoreHPC+Access+Primer

https://it.ucsf.edu/how-to/fac-drive-mapping-instructions?check_logged_in=1#linux

smb://capstorage.fac.ucsf.edu/CX900007_DS1. lab storage
/mnt/fac/CX900007_DS1 fac

* tiny.ucsf.edu/getfac - this is how you file tickets for FAC.

our shared storage is on /home/remote/jirwin3/fac
It is 1 TB. It is group writable for our group and our group alone.

[[Category:Cluster]]

Cluster 8

2026-08-11T17:48:48Z

Frodo: asdf

SEA26

2026-08-07T16:51:03Z

Frodo: asdf

This is the documentation for the new version of SEA by Yujin Wu and Khanh Tang.

== explanation of all the columns ==

== explanation of all the colors ==

== narration of one or two examples to show how to use it ==

== explanation of all menu items ==

== explanation of how to use compounds vs targets ==

== FAQ ==

== Data sources ==

== Software is open source ==
(link to github?)

== how to do an alignment ==
* co-fold the query ligand and separately a similar ligand
* download both to your computer (takes 10 mins +)
* use chimeraX (UCSF ChimeraX) to load the CIF file of each
* use matchmaker #2 #1 to align the proteins
* use select ligand to focus on the ligand.
* visually inspect the query ligand and the most similar annotated ligand.
* do they occupy the same space?
* do they interact with the same residues?
* do the small molecules align in the part of the molecule that is recognized by the protein?
* evaluate whether it seems likely that this prediction is correct? that your query ligand would be expected to recapitulate the same interactions as a known ligand.
* check also for any available experimental structures in the PDB and consider aligning them.
[[Category:SEA]]

ZINC26:Help

2026-07-27T05:07:20Z

Frodo: asdf

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.

== How to use the Interface ==

=== Batch interface ===
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]].

=== Interactive interface ===
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.

== Organization ==
* Top level: Purchasable and Bioactive
* within purchasable:
** aristoStock - our preferred sources for inStock
** aristoDemand - our preferred sources for onDemand
** bBlocks - building blocks for synthesis
** commons - chemistry commons
** covalent - covalent
** inStock
** onDemand
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

== Current Contents and Status of Databases ==
* [[ZINC26:Databases]]

== More notes ==

* 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.
* You must complete a captcha each time you open a new window to protect us from bots.
* We throttle usage in various ways that allow us to offer a free public service without overloading.

== Questions I can ask ==

Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

* what are the most similar molecules I can purchase?
* what are the most similar molecules I can purchase from a given vendor (within a particular HAC range)?
* Does vendor X even sell compounds that look like my compound?
* what is the nearest drug to my compound?
* what is the nearest ChEMBL bioactive 1uM or better to my compound, and what target is it annotated for?
* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
* what is the nearest natural product to my compound?
* what is the nearest metabolite to my compound?
* more to follow (food, etc)

== Updates / Status ==
* writing paper
* checking everything
* testing
* we need to create/update the "All-" databases

== Report Problems / Suggestions ==
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9
* Send us catalogs that you do not see indexed.

== Additional access with login ==
If you login, you get extra access. This includes:
* being able to search 10 SMILES at a time in batch instead of 1.
* access to Arthor
* access to Synthons

== Work in progress ==
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.

[[Category:ZINC26]]
[[Category:JJI]]

AB3:Synthons

2026-07-25T22:52:27Z

Frodo: asdf

Synthons are available at files.docking.org/synthons/

These are synthons for the chemistry commons.
They are organized by purchasability, two other criteria as follows.

We have "all" which includes all purchasable BB at a given price. We also have achiral, which contains molecules that do not have a chiral center, which can simplify early testing.

By price, we organize both cumulatively, and in incremental groups.
The price levels (all for a minimum of 1g) are
* 0-$50
* 50.1-$100
* 100.1-$250
* 250.1-$500
* 500.1-$1000
* fastMADE
* MADE

These are available both cumulatively in individual price baskets. Thus it is easy to request:

* use reagents up to a price of $250 each (say)
* All reagents should be $250 or less, except one may be, say fastMADE.

[[Category:AB3]]
[[Category:JJI]]

ZINC26:Help

2026-07-24T18:38:21Z

Frodo: asdf

This is the help page for ZINC26. It is written specifically as guidance for using the interactive and batch features of ZINC26. Other information about ZINC26 can be found via the [[ZINC26]] page.

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.

== How to use the Interface ==

=== Batch interface ===
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]].

=== Interactive interface ===
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.

== Organization ==
* Top level: Purchasable and Bioactive
* within purchasable:
** aristoInStock - our preferred sources for inStock compounds
** aristoOnDemand - our preferred sources for onDemand compounds
** bBlocks - building blocks for synthesis
** commons - chemistry commons
** covalent - covalent
** inStock
** onDemand
** Sundry
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

== Current Contents and Status of Databases ==
* [[ZINC26:Databases]]

== More notes ==

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.

We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

== Questions I can ask ==

Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

* what are the most similar molecules I can purchase?
* what are the most similar molecules I can purchase from a given vendor (within a particular HAC range)?
* Does vendor X even sell compounds that look like my compound?
* what is the nearest drug to my compound?
* what is the nearest ChEMBL bioactive 1uM or better to my compound, and what target is it annotated for?
* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
* what is the nearest natural product to my compound?
* what is the nearest metabolite to my compound?
* more to follow (food, etc)

== Updates / Status ==
* writing paper
* checking everything
* testing
* we need to create/update the "All-" databases

== Report Problems / Suggestions ==
* Use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9
* Send us catalogs that you do not see indexed.

[[Category:ZINC26]]
[[Category:JJI]]

ZINC26:Databases

2026-07-24T18:34:18Z

Frodo: /* Catalogs included in Batch search */ asdf

Here are the databases currently included in ZINC26, as well as which are included in batch searches.

== Purchasable Catalogs in ZINC26 ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules.
|-
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)
|-
| WuXi || GalaXi || 29B || must check || July 2026
|-
| OnePot || 20M || 20B || expecting update this week || comments
|-
| XtalPi || VAST || 20B || good || comments
|-
| Various || In Stock || 20M || needs updating || see table below
|-
| Various || Covalent || 20M || needs updating || see table below
|-
| Various || BB || 20M || needs updating || see table below
|-
| - || Total || 100B ||
|}

== Annotated Catalogs in ZINC26 ==

{| class="wikitable"
|-
! Category !! Catalog !! size !! date !! comments
|-
| inVitro || ChEMBL 36 1uM || 700K || July 2025 || other constraints apply
|-
| inVivo || DrugBank || 10K || March 2026 || update annually or better
|-
| Natural || Cocounut || 715K || May 2026 || update quarterly if possible
|-
| Natural || catalog2 || xx || xx || xx
|-
| Total || 1M ||
|}

== Catalogs included in Batch search ==

{| class="wikitable"
|-
! Batch Category !! # files !! size !! Catalogs
|-
| Purchasable || 51 || 300B || Enamine REAL, ChemSpace FS5, WuXi GalaXi,
|-
| Bioactive || 3 || 1M || Drugbank, ChEMBL 1uM, Coconut, other NP
|-
|}

== In-Stock Catalog detail ==

We have 100s of vendors.

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Various || In Stock || 20M || needs updating || see table below
|-
| Various || Covalent || 20M || needs updating || see table below
|-
| Various || BB || 20M || needs updating || see table below
|-
| - || Total || 100B ||
|}

== BB Catalog Detail ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Chem-Space|| In-Stock || 500K ||
|-
| MolPort || In-Stock || 2M ||
|-
| Enamine|| FastMADE || 120M ||
|-
| Enamine || MADE | 1.35B ||
|-
| - || Total || 100B ||
|}
Question: how many BB are there that are not covered by the above: Molport+ChemSpace+MADE ?
We don't know, but we will find out.

== Covalent Catalog Detail ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Enamine || Covalent || 1B
|-
| - || Total || 1B ||
|}
So far, Enamine is the only reliable covalent vendor. There are in stock and on demand compounds.
Let's add any other covalent vendors here, but warhead. Maybe we can fish them out of commercially available compounds?

[[Cluster_7:Libraries]]

Back to [[ZINC26:Help]]
[[Category:ZINC26]]

ZINC26:Databases

2026-07-24T18:28:38Z

Frodo: /* Purchasable Catalogs in ZINC26 */ asdf

ZINC26:Databases

2026-07-24T18:27:28Z

Frodo: /* Purchasable Catalogs in ZINC26 */ asdf

ZINC26:Databases

2026-07-24T18:26:22Z

Frodo: /* Catalogs included in Batch search */ asdf

ZINC26:Databases

2026-07-24T18:23:44Z

Frodo: asdf

ZINC26:Databases

2026-07-24T18:22:56Z

Frodo: asdf

Here are the databases currently included in ZINC26, as well as which are included in batch searches.

== Status of Purchasable Catalogs in ZINC26 ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules.
|-
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)
|-
| WuXi || GalaXi || 29B || must check || July 2026
|-
| OnePot || 20M || 20B || expecting update this week || comments
|-
| XtalPi || VAST || 20B || good || comments
|-
| Various || In Stock || 20M || needs updating || comments
|-
| Total || 5.003 B ||
|}

== Status of Annotated Catalogs in ZINC26 ==

{| class="wikitable"
|-
! Category !! Catalog !! size !! date !! comments
|-
| inVitro || ChEMBL 36 1uM || 700K || July 2025 || other constraints apply
|-
| inVivo || DrugBank || 10K || March 2026 || update annually or better
|-
| Natural || Cocounut || 715K || May 2026 || update quarterly if possible
|-
| Natural || catalog2 || xx || xx || xx
|-
| Total || 1M ||
|}

== When you search ZINC26 in batch, you search the following ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules.
|-
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)
|-
| WuXi || GalaXi || 29B || must check || July 2026
|-
| OnePot || 20M || 20B || expecting update this week || comments
|-
| XtalPi || VAST || 20B || good || comments
|-
| Various || In Stock || 20M || needs updating || comments
|-
| Total || 5.003 B ||
|}

[[Cluster_7:Libraries]]

Back to [[ZINC26:Help]]
[[Category:ZINC26]]

ZINC26:Databases

2026-07-24T17:15:51Z

Frodo: asdf

Here are the databases currently in ZINC26, and their status.

== Contents of ZINC26 ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules.
|-
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)
|-
| WuXi || GalaXi || 29B || must check || July 2026
|-
| OnePot || 20M || 20B || expecting update this week || comments
|-
| XtalPi || VAST || 20B || good || comments
|-
| Various || In Stock || 20M || needs updating || comments
|-
| Total || 5.003 B ||
|}

== When you search ZINC26 in batch, you search the following ==

{| class="wikitable"
|-
! Vendor !! Catalog !! size !! status !! Date
|-
| Enamine || REAL|| 72B || 33.8M (14.7M unique) || "only" 1 B "squeaky clean" molecules.
|-
| Chem-Space || Freedom Space 5 || 30B || 248M (105M unique)
|-
| WuXi || GalaXi || 29B || must check || July 2026
|-
| OnePot || 20M || 20B || expecting update this week || comments
|-
| XtalPi || VAST || 20B || good || comments
|-
| Various || In Stock || 20M || needs updating || comments
|-
| Total || 5.003 B ||
|}

[[Cluster_7:Libraries]]

Back to [[ZINC26:Help]]
[[Category:ZINC26]]

ZINC26:Databases

2026-07-24T17:11:06Z

Frodo: asdf

Here are the databases currently in ZINC26, and their status.

[[Cluster_7:Libraries]]

Back to [[ZINC26:Help]]
[[Category:ZINC26]]

News of 2026-08 Aug

2026-07-24T17:09:36Z

Frodo: asdf

August 2026 news.

* new tools coming on line.
* old tools being maintained

[[Category:News]]

News of 2026-07 Jul

2026-07-24T17:08:50Z

Frodo: asdf

Work in progress: July 2026.

* zinc26.docking.org pre-release for testing.
* assembly of new BB based on Chem-Space, Molport, FastMADE and MADE for retrosynthesis and synthon docking.
* new sea.docking.org ready for testing
* new captchas to keep it real.
* in progress: EBCL. commons.

[[Category:Databases]]
[[Category:News]]

Category:News

2026-07-24T17:07:16Z

Frodo: asdf

When there are major changes or rearrangements, we create a "News" page and link it here. Date is YYYY-MM. Latest news is [[News of 2026-07 Jul]]

User talk:Mdruch

2026-07-24T17:04:17Z

Frodo: Welcome!

'''Welcome to ''DISI''!'''
We hope you will contribute much and well.
You will probably want to read the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents help pages].
Again, welcome and have fun! [[User:Frodo|Frodo]] ([[User talk:Frodo|talk]]) 17:04, 24 July 2026 (UTC)

User:Mdruch

2026-07-24T17:04:17Z

Frodo: Creating user page for new user.

new graduate student in shoichet lab

User talk:Dgc

2026-07-24T17:03:10Z

Frodo: Welcome!

User:Dgc

2026-07-24T17:03:10Z

Frodo: Creating user page for new user.

Computer scientist with strong interest in drug discovery. Computational applications include data mining of large drug screening databases.

User talk:Abel

2026-07-24T17:02:51Z

Frodo: Welcome!

User:Abel

2026-07-24T17:02:51Z

Frodo: Creating user page for new user.

I am a Pharmaceutical Chemist (QFB) and researcher with expertise in medicinal chemistry, computational drug discovery, molecular docking, virtual screening, and ADMET prediction. My research focuses on the identification and optimization of bioactive compounds from natural products and synthetic libraries against therapeutic targets associated with infectious diseases, inflammation, and metabolic disorders. I use structure-based drug design, molecular modeling, and cheminformatics to prioritize compounds for experimental validation. I also serve as a university professor, teaching medicinal chemistry, pharmacology, biochemistry, and computational chemistry.

ZINC26:Help

2026-07-24T16:59:40Z

Frodo: asdf

This is the help page for ZINC26. It is written specifically as guidance for using the interactive and batch features of ZINC26. Other information about ZINC26 can be found via the [[ZINC26]] page.

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.

== Batch interface ==
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]].

== Interactive interface ==
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.

== Organization ==
* Top level: Purchasable and Bioactive
* within purchasable:
** aristoInStock - our preferred sources for inStock compounds
** aristoOnDemand - our preferred sources for onDemand compounds
** bBlocks - building blocks for synthesis
** commons - chemistry commons
** covalent - covalent
** inStock
** onDemand
** Sundry
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

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.

We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

* what are the most similar molecules I can purchase?
* what are the most similar molecules I can purchase from a given vendor (within a particular HAC range)?
* Does vendor X even sell compounds that look like my compound?
* what is the nearest drug to my compound?
* what is the nearest ChEMBL bioactive 1uM or better to my compound, and what target is it annotated for?
* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
* what is the nearest natural product to my compound?
* what is the nearest metabolite to my compound?
* more to follow (food, etc)

[[Category:ZINC26]]
[[Category:JJI]]

== When I search ZINC26 purchasable in batch, what am I really searching? ==

* here is a page that describes what is currently searched [[ZINC26:Databases]]

== Updates / Status ==
* As of July 2, 2026, zinc26 is in production at zinc26.docking.org.
* We have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon-based libraries will be enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quite there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer.
* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

== how to report suggestions / problems ==
Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9

* Please send us catalogs that you do not see indexed.

[[Category:ZINC26]]

ZINC26:Help

2026-07-24T00:36:15Z

Frodo: /* Organization */ asdf

This is the help page for ZINC26. It is written specifically as guidance for using the interactive and batch features of ZINC26. Other information about ZINC26 can be found via the [[ZINC26]] page.

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.

== Batch interface ==
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]].

== Interactive interface ==
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.

== Organization ==
* Top level: Purchasable and Bioactive
* within purchasable:
** aristoInStock - our preferred sources for inStock compounds
** aristoOnDemand - our preferred sources for onDemand compounds
** bBlocks - building blocks for synthesis
** commons - chemistry commons
** covalent - covalent
** inStock
** onDemand
** Sundry
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

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.

We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

* what are the most similar molecules I can purchase?
* what are the most similar molecules I can purchase from a given vendor (within a particular HAC range)?
* Does vendor X even sell compounds that look like my compound?
* what is the nearest drug to my compound?
* what is the nearest ChEMBL bioactive 1uM or better to my compound, and what target is it annotated for?
* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
* what is the nearest natural product to my compound?
* what is the nearest metabolite to my compound?
* more to follow (food, etc)

[[Category:ZINC26]]
[[Category:JJI]]

== Updates / Status ==
* As of July 2, 2026, zinc26 is in production at zinc26.docking.org.
* We have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon-based libraries will be enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quite there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer.
* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

== how to report suggestions / problems ==
Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9

* Please send us catalogs that you do not see indexed.

[[Category:ZINC26]]

Building blocks 2026

2026-07-22T18:47:29Z

Frodo: asdf

I have prepared some building blocks for retrosynthesis and other applications.

The BB were prepared as follows.

* we got ChemSpace (CS) and Molport (MP), two outstanding building block suppliers who were able to provide sufficient information for us to proceed.
* we break up into price range, 0-50, 50-100, 100-250, 250-500, 500-100 and then fastMADE and MADE.
* we remove molecules where there is less than 1g of stock available, or information is unknown.
* we desalt, canonicalize, and remove duplicates, and remove invalid SMILES.
* anything that fails RDKit kekulization was eliminated
* we begin with CS 0-50 and add MP 0-50 molecules not found in CS 0-50.
* then we add CS 50.1-100 and then MP 50.1-100.
* repeat with 100-250, 250-500, 500-1000, and then fastMADE and then MADE.
* these databases are then indexed in Smallworld and Arthor.
* these databases are also processed for Chemistry Commons.
* the numbers are: max price, total cumulative unique, of which from CS, of which from MP)
* 50, 253,000, 50,000, 200,000
* 100, 200,000, 50,000, 50,000
* 250, 200,000, 50,000, 50,000
* 500, 200,000, 50,000, 50,000
* 1000, 100,000, 50,000, 50,000
* fastMade, 100,000,000, 0, 0
* MADE, 1,000,000,000, 0,0

[[Category:BB]]
[[Category:JJI]]

Category:Cluster

2026-07-17T20:20:26Z

Frodo: asdf

== Current Usage Narrative ==

As of July 17, 2026:
* Cluster 2 is your default choice for local compute. Most things work here.
* Cluster 3 aka Wynton is your default for "at scale" calculations. Most of ZINC and most software is here. Cluster 3 will be going away in 2027. We'
're not sure exactly when.
* Cluster 7 should be your default choice for local compute, except it still lacks some features and software. This is the cluster that will grow most between now and 2030 assuming we survive our leaders.
* Cluster 8 will be your default choice for "at scale" calculations by 2027. For now, you can get access, and there is spare capacity.
* Cluster 0 still exists, but is "legacy" and is being wound up.
* Cluster 6 aka Keiser still exists, but is "legacy" and is being wound up.
* Cluster 1 has not existed since 2014. ixnay onyay ethay uestionsqay.

== Set up your own cluster ==
see: [[So you want to set up a lab]]

== New group members ==
please use [[Cluster 7]].
Most group members as of Feb 2026 are using [[Cluster 2]].
A few are using [[Cluster 7]], just ask us. Cluster 8 (coreHPC) is available.
[[cluster exceptions|exceptions]].

** the cpu/gpu and disk spaces are guesses and no effort has been made to make them accurate. If you know the correct numbers, please update and indicate this **

{| class="wikitable"
|-
! Cluster ID !! Description !! How to get started || cpu/gpu || Disk space || Notes
|-
| [[Cluster 0]] || Legacy UCSF cluster || Closed || 300/0 || 20 TB || Legacy support. Retire asap.
|-
| [[Cluster 1]] || Toronto Cluster || Closed|| 448/0 ||40 TB || Defunct
|-
| [[Cluster 2]] || New UCSF cluster || Closed || 800/52 || 6.5 PB || No new growth. Merge into Cluster 7
|-
| [[Cluster 3]] || [https://salilab.org/qb3cluster UCSF Shared Cluster] aka Wynton || Closed || 18,000/250 || 6 PB || Wynton is end of life. Merging with cluster 8.
|-
| [[Cluster 5]] || [https://aws.amazon.com/ Amazon Cloud] || ask John || unlimited || unlimited || Commercial. Ask us. Watch out for bandwidth costs.
|-
| [[Cluster 6]] || Mike Keiser cluster || Closed || 100/50 || 1 PB || End of life. being merged into cluster 7
|-
| [[Cluster 7]] || New Cluster 7 || JJ/Khanh || 100/8 || 1 PB || Future main private cluster for our group
|-
| [[Cluster 8]] || FAC/coreHPC || UCSF IT || 16,000/350 || 1 PB || UCSF replacement for Wynton
|-
| [[Cluster 9]] || Offsite experimental cluster || John || 64/4 || 1 PB || off-site cluster
|}

Access our clusters from [[Lab Security Policy | secure machines]] only. If unsure, ask the [[sysadmin]]s.

[[Category:Internal]]
[[Category:Topic]]

User talk:Chris Flores

2026-07-16T18:59:33Z

Frodo: Welcome!

User:Chris Flores

2026-07-16T18:59:33Z

Frodo: Creating user page for new user.

Chris joined the BKS lab in the summer of 2026, as the new Junior Specialist / Lab Manager, after having graduated from Williams College.

Category:Serge

2026-07-09T20:44:15Z

Frodo: asdf

Things Serge worked on summer of 2026.

Qsar

2026-07-09T20:44:03Z

Frodo: asdf

== Synopsis ==

This guide will detail the installation and usage of Qsar (https://github.com/syedzayyan/qsar-in-browser) on cluster 7.

Last updated on July 9th, 2026. Things may change with time, so don't trust this guide after a long time has passed.

== Installation and Running ==

First, clone the Qsar repo off of github into your chosen folder and cd into it.

<code>
git clone https://github.com/syedzayyan/qsar-in-browser.git

cd qsar-in-browser
</code>

Then, create a new conda environment followed by a nodejs installation after loading anaconda3.

<code>
ml anaconda3

conda create -n qsar

conda activate qsar

conda install conda-forge::nodejs
</code>

Finally, install the dependencies and run the website.

<code>
npm install

npm run dev
</code>

This will start qsar on http://localhost:3000 of the machine that you've started it on.

You may now use an SSH portal and a browser proxy add-on such as SwitchyOmega to remotely connect to the localhost website. If you don't know how to do so, follow the relevant guides on this wiki or ask a lab member.

[[Category:Serge]]

ZINC26

2026-07-08T17:53:35Z

Frodo: asdf

== Introduction ==
ZINC26 is a search tool for purchasable chemical space. It uses Smallworld and Arthor technology from NextMove Software to allow searching billions of molecules in seconds. There is a batch interface and an interactive one.

* help page: [[ZINC26:Help]]

The new database is organized around a set of [[ZINC26:Principles | principles]].

== API ==
* zinc26dev.docking.org/docs describes how to use. Here is a short tutorial to get you started.

== Coming soon ==
* 3d database builder
* additional data

== Tutorial in how to use datawarrior ==
* the columns in datawarrior are as follows.
* we are still working on adding a net_charge column.
* we suggest you proceed as follows.

[[Category:ZINC26]]

ZINC26

2026-07-08T17:52:54Z

Frodo: dfs

== Introduction ==
ZINC26 is a search tool for purchasable chemical space. It uses Smallworld and Arthor technology from NextMove Software to allow searching billions of molecules in seconds. There is a batch interface and an interactive one.

The new database is organized around a set of [[ZINC26:Principles | principles]].

== API ==
* zinc26dev.docking.org/docs describes how to use. Here is a short tutorial to get you started.

== Coming soon ==
* 3d database builder
* additional data

== Tutorial in how to use datawarrior ==
* the columns in datawarrior are as follows.
* we are still working on adding a net_charge column.
* we suggest you proceed as follows.

[[Category:ZINC26]]

ZINC26:Help

2026-07-08T17:50:59Z

Frodo: asD

This is the help page for ZINC26. It is written specifically as guidance for using the interactive and batch features of ZINC26. Other information about ZINC26 can be found via the [[ZINC26]] page.

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.

== Batch interface ==
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]].

== Interactive interface ==
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.

== Organization ==
* Top level: Purchasable and Bioactive
* within purchasable:
** aristoInStock - our preferred sources for inStock compounds
** aristoOnDemand - our preferred sources for onDemand compounds
** bBlocks - building blocks for synthesis
** commons - chemistry commons
** covalent - covalent
** inStock
** onDemand
** Sundry
* within bioactive: inVitro (e.g. ChEMBL), inVivo (e.g. drugs), natural (natural products, metabolites)

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.

We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

* what are the most similar molecules I can purchase?
* what the most most similar molecules I can purchase from a particular vendor (within a particular HAC range)?
* Does vendor X sell compounds that look like my compound?
* what is the nearest drug to my compound?
* what is the nearest chembl bioactive 1uM or better to my compound?
* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
* what is the nearest natural product to my compound?
* what is the nearest metabolite to my compound?

== Updates / Status ==
* As of July 2, 2026, zinc26 is in production at zinc26.docking.org.
* We have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon-based libraries will be enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quite there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer.
* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

== how to report suggestions / problems ==
Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9

* Please send us catalogs that you do not see indexed.

[[Category:ZINC26]]

News of 2026-07 Jul

2026-07-08T17:05:06Z

Frodo: asdf

Work in progress: July 2026.

* zinc26.docking.org is now available for testing
* sea.docking.org is available for testing.

* We are updating catalogs in zinc26.
* chemspace, $50, $100, $200, $300, $400, $500, all. all of these chiral and achiral
* then csall + fastmade, csall+made, and achiral versions of these
* arthor, smallworld. Organize by warhead.
* molport
* EBCL
* fast made and made.
* chemistry commons tools

[[Category:Databases]]
[[Category:News]]

News of 2026-07 Jul

2026-07-08T17:04:13Z

Frodo: asdf

Changes in July 2026.

* updating catalogs in zinc26.
* chemspace, $50, $100, $200, $300, $400, $500, all. all of these chiral and achiral
* then csall + fastmade, csall+made, and achiral versions of these
* arthor, smallworld. Organize by warhead.
* molport
* EBCL

[[Category:Databases]]
[[Category:News]]

ZINC26

2026-07-07T19:30:32Z

Frodo: asdf

== Introduction ==
ZINC26 is a search tool for purchasable chemical space. It uses Smallworld and Arthor technology from NextMove Software to allow searching billions of molecules in seconds. There is a batch interface and an interactive one.

== Batch interface ==
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).
An approach of how to use DataWarrior may be found below.

== Interactive interface ==
ZINC26 has many catalogs of both purchasable and bioactive compounds, which allow many interesting questions to be answered almost instantly.

== Organization ==
* (mostly non-covalent) Screening compounds
* Bioactive compounds (ChEMBL, natural products, drugs, etc)
* Building blocks
* Covalent compounds.
* maybe chemistry commons.

* Within screening compounds, we organize by vendor and heavy atom count (HAC).
* Covalent are organized by warhead
* building blocks are organized by warhead and by vendor
* ChEMBL compounds are organized by target.
* Purchasable are organized by "Plus" (we have had a better experience) and regular.

== Advantages of logging in ==
If you request and use a login (free), you are entitled to additional access:
* search for up to 10 molecules per transaction, not just 1 for anonymous search
* access Arthor to search molecules that can not yet be indexed with Smallworld.
* access the API

The new database is organized around a set of [[ZINC26:Principles | principles]].

== API ==
* zinc26dev.docking.org/docs describes how to use. Here is a short tutorial to get you started.

== Coming soon ==
* 3d database builder
* additional data

== Tutorial in how to use datawarrior ==
* the columns in datawarrior are as follows.
* we are still working on adding a net_charge column.
* we suggest you proceed as follows.

[[Category:ZINC26]]

ZINC26:Help

2026-07-02T18:16:40Z

Frodo: asfd

ZINC26 provides interfaces to search purchasable chemical space and biologically active chemical space.

There are two separate interfaces, interactive (10s turnaround time) and batch (3 mins turnaround time if there is no queue).

The interactive interface searches specific databases subsets you select, from a few to a few billion molecules each. The batch interface searches _all_ purchasable or _all_ bioactive databases in a single transaction.

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.

We throttle usage in other (so far undisclosed) ways that allow us to offer a free public service without overloading.

Collectively, ZINC26 allows "what if" type searches of purchasable and biologically precedented chemical space. It allows the following questions.

* what are the most similar molecules I can purchase?
* what the most most similar molecules I can purchase from a particular vendor (within a particular HAC range)?
* Does vendor X sell compounds that look like my compound?
* what is the nearest drug to my compound?
* what is the nearest chembl bioactive 1uM or better to my compound?
* what is the nearest ligand for some gene product, say DRD4, 1uM or better, to my compound?
* what is the nearest natural product to my compound?
* what is the nearest metabolite to my compound?

== Updates / Status ==
* As of July 2, 2026, zinc26 is in production at zinc26.docking.org and zinc26dev.docking.org. If you cannot get in, write us at jjiteam at googlegroups dot com for access.
* we have indexed most of the commercially available libraries that are distributed as enumerated libraries. Synthon based libraries will enumerated, but it takes time (ask the vendor to enumerate up to HAC29 and send it to us, and we will index it)
* We are aiming to offer "all purchasable to HAC29" and "all bioactives" as one-click interactive databases. So far, we are not quiet there, but we are close. Use the batch interface until that is ready. It may turn out that we need to offer
* all-purchasable-to-HAC25, and then one by one by HAC after that, in order to provide good interactive service. But we are trying to do it to HAC29.

== how to report suggestions / problems ==
Please use our usual form for reporting problems: https://forms.gle/LZV1FCmLWxUWznVi9

* Please send us catalogs that you do not see indexed.

[[Category:ZINC26]]

SEA26

2026-07-02T17:08:16Z

Frodo: asdf

Category:ZINC26

2026-07-01T15:47:05Z

Frodo: asdf

Link all ZINC26 related articles together.

ZINC26:API

2026-07-01T15:46:41Z

Frodo: asdf

Here is how to use the ZINC26 API.

Documentation is at zinc26dev.docking.org/docs/

Examples of how to use it. This may change as it develops, and may change as login/authentication is incorporated.

[[Category:JJI]]
[[Category:ZINC26]]

Looping solution

2026-06-30T22:48:19Z

Frodo: asdf

= Looping Solution =

Here is our approach to running jobs at scale on coreHPC.

* 1. on cluster 7 there is a directory with job control language
* 2. there is a cronjob that runs on corehpc.
* 3. once an hour, it iterates over all jobs in the system, and moves them forward.
* 4. the job status of each job is below.
* 5. the supported job control language is below.

== job status ==
* 0 new job request
* 1 job data has started copying to fac
* 2 job data copy to fac has completed successfully
* 12 job data copy to fac failed (and requires attention)
* 3 job has been submitted on coreHPC
* 4 job is running on coreHPC
* 5 job has completed on coreHPC
* 15 job has failed in coreHPC (and requires attention)
* 6 scp of job results to C7 has started
* 7 scp of job results to C7 has completed normally
* 17 scp of job results to C7 has failed (and requires attention)

== supported job control language (JCL) ==

* Each job has a file. The command syntax is as follows
type: docking, chemstep, other
dockfiles: /nfs/exe/work/jji/projects/target1/dockfiles (includes INDOCK)
tranches: /nfs/exe/work/jji/projects/target1/tranches (one file per jobs, circa 1 TB each)

[[Category:JJI]]

Cluster 8

2026-06-30T22:39:30Z

Frodo: asdf

Standup tuesday

2026-06-30T16:39:38Z

Frodo: asdf

* 12 - 12.30 min 1 to max 5 mins per person

This meeting will be by zoom and in person when possible.
If you are not available, no worries, but please send me a short email with what you've done in the last week and what you plan for the coming week.

[[Category:JJI]]

Chemspace API

2026-06-29T21:54:56Z

Frodo: asdf

This is a quick guide on how to use Chemspace API to get pricing information. Link to Chem-space's API https://api.chem-space.com/docs/
== Email info@chem-space.com to obtain API Key ==
== Get Access Token ==
Now that you have obtained the access token. You will use the command below to get the API Key (please replace <API Key> with your own API Key)
curl -X GET \
"https://api.chem-space.com/auth/token" \
-H "Accept: application/json" \
-H "Authorization: Bearer <API Key>"
* Output will look like this
{"access_token":"<access_token>",
"expires_in":3600,
"api_key":"<API Key>" }
<b>API key and access_token are not the same. API Key can only be used to obtain access token. Access token expires in 1 hour.</b>
== Search ==
Here is a list of catalogs searchable on Chem-Space and their identifiers. You can look up more than one catalogs by specified them under categories argument separated by comma
CSSS (In-stock Screening Compounds)
CSMS (Make-On-Demand Screening Compounds)
CSCS (Custom Request)
CSSB (In-Stock Building Blocks)
CSMB (Make-On-Demand Building Blocks)
=== By Exact Smiles ===
Example (look up exact CC(N)=O from Custom Request and Make-On-Demand BB catalogs) :
curl -X POST \
"https://api.chem-space.com/v3/search/exact?count=3&page=1&categories=CSCS,CSMB" \
-H "Accept: application/json; version=3.1" \
-H "Authorization: Bearer <access_token>" \
-H "Content-Type: multipart/form-data" \
-F "SMILES=CC(N)=O"

=== By Substructure ===
Example:
curl -X POST \
"https://api.chem-space.com/v3/search/sub?count=3&page=18&categories=CSSB,CSCS" \
-H "Accept: application/json; version=3.1" \
-H "Authorization: Bearer <access_token>" \
-H "Content-Type: multipart/form-data" \
-F "SMILES=CC(N)=O"

=== By Similarity ===
Example:
curl -X POST \
"https://api.chem-space.com/v3/search/sim?count=2&page=6&categories=CSSS,CSMS" \
-H "Accept: application/json; version=3.1" \
-H "Authorization: Bearer <access_token>" \
-H "Content-Type: multipart/form-data" \
-F "SMILES=CC(N)=O"
=== By Compound ID ===
It can look up by
* CSMB00000000001 - Chemspace ID
* CSC000000065 - old Chemspace ID
* 60-35-5 - CAS
* MFCD06217521 - MFCD
* CSC1=NN=NN1C - SMILES
* BBV-32027078 - vendor ID
Example:
curl -X POST \
"https://api.chem-space.com/v3/search/text?count=3&page=2&categories=CSMB" \
-H "Accept: application/json; version=3.1" \
-H "Authorization: Bearer <access_token>" \
-H "Content-Type: multipart/form-data" \
-F "query=CSMB00000000001, CSC000000065, 60-35-5, MFCD06217521, CSC1=NN=NN1C, BBV-32027078"

[[Category:JJI]]
[[Category:API]]

Datagrok

2026-06-29T21:53:27Z

Frodo: asdf

https://github.com/datagrok-ai/public/blob/master/packages/Chem/README.md

figure out how to use this.

[[Category:JJI]]

Category:Huggingface

2026-06-29T21:52:38Z

Frodo: asdf

Links to things we do on huggingface

Category:ADMET

2026-06-29T21:52:21Z

Frodo: asdf

links for ADMET calculations

OpenADMET on huggingface

2026-06-29T21:52:06Z

Frodo: asdf

This page is all about openADMET on huggingface.

https://huggingface.co/spaces/openadmet/prediction_portal

https://huggingface.co/spaces/jir322/prediction_portal

[[Category:JJI]]
[[Category:ADMET]]
[[Category:Huggingface]]

Cluster 9

2026-06-29T17:56:59Z

Frodo: asdf

Off-site experimental cluster.

[[Category:Cluster]]