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Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. | Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". We hope you find what you are looking for, but if not, it is editable. Just login and [[contribute | edit it and help us improve]] (please). This wiki aims to serve several [[:Category:Roles | constituencies]]. It remains a work in progress. [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing]. For personalized help, attend [[Weekly office hours]]. For what's new, please see [[:Category:News | News of changes]] | ||
== Popular software and databases == | == Popular software and databases == | ||
| Line 8: | Line 8: | ||
! Main article !! Description !! Notes/Links | ! Main article !! Description !! Notes/Links | ||
|- | |- | ||
| [[:Category:DOCK |DOCK]] || Our molecular docking software || | | [[: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 || [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22] | | [[: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] | | [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org] | ||
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| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR] | | [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR] | ||
|- | |- | ||
| [[Chemistry commons]] ||Chemistry commons || [https://commons.docking.org | | [[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] | | [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org] | ||
|} | |||
== Subject areas == | |||
{| class="wikitable" | |||
|- | |||
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] | |||
|| [[Hit picking party]] || [[Excipients]] || [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] | |||
|} | |} | ||
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{| class="wikitable" | {| 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]] | ||
|- | |- | ||
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]] | |||
|} | |||
== Organizational pages == | |||
{| class="wikitable" | |||
|- | |- | ||
| [[:Category: | | [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]] | ||
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] | || [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || ZZ | ||
|- | |- | ||
| [ | | [[:Category:Roles | Who are you?]] || [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]] | ||
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | manuals, as they are ]] | |||
|} | |} | ||
Revision as of 20:26, 23 May 2024
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the Shoichet Lab and Irwin Lab at UCSF. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". We hope you find what you are looking for, but if not, it is editable. Just login and edit it and help us improve (please). This wiki aims to serve several constituencies. It remains a work in progress. Tell us how we are doing. For personalized help, attend Weekly office hours. For what's new, please see News of changes
Popular software and databases
| 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 |
Subject areas
| Databases | Molecular Docking | Colloidal aggregation | Model systems | Hit picking party | Excipients | Systems pharmacology | Covalent docking |
Other Starting Points
| Lab members with ssh | Non members without ssh | Assaying Compound Activity |
| Run on our servers | Run on your servers | |
| programmatic access (API) | Software | Aggregator advisor |
Organizational pages
| Topics | Who are you? | Idioms | Article type | Attributes | ZZ |
| Who are you? | Categories | Tutorials | Problems | FAQ | manuals, as they are |
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. If our servers appear down or broken and we have not communicated this, we would be grateful to be told via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461
If you have a problem or a question, we always like to hear about it. Tell us how we are doing. More about ways to communicate with us.
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.