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Welcome to [[ | Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. Our software and databases may be found via [https://docking.org docking.org]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology, and serves several [[:Category:Roles | constituencies]]. If you are a <b>new member of a lab</b>, please see the [[Welcome group members | following guide]]. Docking documentation [https://docs.docking.org docs.docking.org] | ||
[[:Category: | === Relevant Links === | ||
* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form] | |||
* [[:Category:News | News]] | |||
* [[Group Meeting | Group Meeting Times]] | |||
* [https://x.com/chem4biology/ Outages and Updates] | |||
* [https://discord.gg/4MpD6UF5AN Chat on Discord] | |||
= | == Are you new here? == | ||
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, in academia, non-profits and in pharma and biotech. We work in five major technology areas: | |||
* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). [[DOCK]] | |||
* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. [[Smallworld]] and [[Arthor]]. | |||
* 3) '''Target prediction'''. Given a molecule, our program [[SEA]] can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action"). | |||
* 4) '''Bespoke Chemistry'''. The [[Chemistry Commons]] is a platform to help chemists and biologist to collaborate. This system allows chemists to define which molecules their new chemistry can access, and it allows biologists to search through this novel bespoke chemistry. | |||
* 5) '''Chemical Libraries'''. [[ZINC]] is available for download in 2D and 3D. | |||
We hope you find this website interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support. | |||
== | == Products == | ||
{| class="wikitable" | |||
|- | |||
! Main article !! Description !! Notes/Links | |||
|- | |||
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org] | |||
|- | |||
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22] | |||
|- | |||
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org] | |||
|- | |||
| [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate] | |||
|- | |||
| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR] | |||
|- | |||
| [[Chemistry Commons]] ||Chemistry Commons || [https://commons.docking.org Chemistry Commons] | |||
|- | |||
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org] | |||
|} | |||
== | == Topics == | ||
{| class="wikitable" | |||
|- | |||
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]] | |||
|| [[Hit picking party]] | |||
|- | |||
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]] | |||
|- | |||
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] || | |||
|} | |||
== | == Other topics == | ||
{| class="wikitable" | |||
|- | |||
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]] | |||
|- | |||
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]] | |||
|- | |||
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]] | |||
|} | |||
== | == Organizational == | ||
{| class="wikitable" | |||
|- | |||
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]] | |||
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]] | |||
|- | |||
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]] | |||
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]] | |||
|} | |||
Still haven't found what you're looking for? Try the search bar top right to see if that works... | |||
[[Category: | = Outages and Support = | ||
* We communicate about outages and updates via [https://twitter.com/chem4biology X]. | |||
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server] | |||
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937 one four six one | |||
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing]. | |||
* More about ways to [[feedback | communicate with us]]. | |||
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free. | |||
= Policies, Privacy and all that = | |||
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our [[DISI:Privacy_policy|privacy policy]]. | |||
[[Category:FAQ]] | |||
[[Category:Public]] | |||
[[Category:Organization]] | |||
[[Category:Navigation]] | |||
Latest revision as of 17:53, 22 May 2025
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the Shoichet Lab and Irwin Lab at UCSF. Our software and databases may be found via docking.org. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology, and serves several constituencies. If you are a new member of a lab, please see the following guide. Docking documentation docs.docking.org
Relevant Links
Are you new here?
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, in academia, non-profits and in pharma and biotech. We work in five major technology areas:
- 1) Molecular docking screens take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). DOCK
- 2) Analog-by-catalog works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. Smallworld and Arthor.
- 3) Target prediction. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").
- 4) Bespoke Chemistry. The Chemistry Commons is a platform to help chemists and biologist to collaborate. This system allows chemists to define which molecules their new chemistry can access, and it allows biologists to search through this novel bespoke chemistry.
- 5) Chemical Libraries. ZINC is available for download in 2D and 3D.
We hope you find this website interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.
Products
| Main article | Description | Notes/Links |
|---|---|---|
| DOCK | Our molecular docking software | There are two main branches. The latest are DOCK 3.8 and DOCK 6.11 dock.docking.org |
| ZINC | Commercially available compounds | There are two databases zinc20 zinc22 |
| SEA | Similarity Ensemble Approach | Drug repurposing, target identification, phenotypic screening. sea.bkslab.org |
| DUDE Family | Benchmarks for docking | dude.docking.org/generate |
| TLDR | TLDR is a Ligand Discovery Resource | TLDR |
| Chemistry Commons | Chemistry Commons | Chemistry Commons |
| DOCK Blaster | A public access service for docking screens | blaster.docking.org |
Topics
| Databases | Molecular Docking | Colloidal aggregation | Hit picking party |
| Systems pharmacology | Covalent docking | Chemical Space | Decoys |
| Fragment Docking | Excipients | Model systems |
Other topics
| Lab members with ssh | Non members without ssh | Assaying Compound Activity |
| Run on our servers | Run on your servers | Set up a lab |
| programmatic access (API) | Software | Aggregator advisor |
Organizational
| Topics | Who are you? | Idioms | Article type | Attributes | Policies |
| Categories | Tutorials | Problems | FAQ | Manuals | Jargon |
Still haven't found what you're looking for? Try the search bar top right to see if that works...
Outages and Support
- We communicate about outages and updates via X.
- We have open conversations among ourselves and with users on our discord server. discord server
- If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937 one four six one
- Tell us how we are doing.
- More about ways to communicate with us.
- Weekly office hours. 11 am PT is the 'daily' office hours on discord, if we are free.
Policies, Privacy and all that
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our privacy policy.