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{| class="wikitable"
{| class="wikitable"
|-
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| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]]   ||  [[:Category:Docking|Molecular Docking]]
| [[Welcome group members | Lab members with ssh]] || [[:Category:Databases | Databases]] ||  [[:Category:Docking|Molecular Docking]]
  || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]]
  || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]]  
|-
|-
| [[Welcome group members | Lab members with ssh]] || [[Hit picking party]] || [[TLDR]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]] || [[:Category:API | programmatic access (API) ]]  
| [[Hit picking party]] || [[TLDR]] || [[Assaying Compound Activity]] || [[:Category:API | programmatic access (API) ]] || [[Welcome web user | Non members without ssh ]]  
|-
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| [[Welcome web user | Non members without ssh ]] || [[:Category:Software|Software ]] || [[:Category:Databases | Databases]] || [[Excipients]] || [[Aggregator advisor]] || xxxx
| [[:Category:Software|Software ]] || [[Excipients]] || [[Aggregator advisor]] || [[:Category:Manual | manuals, as they are ]] || [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]]
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== Organizational pages ==
{| class="wikitable"
|-
|-
| [[:Category:Manual | manuals, as they are ]] || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] || [[:Category:Systems pharmacology | Systems pharmacology]]  
| [[: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]]
|-
|| [[:Category:Roles | Who are you?]] || [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]]  
| [https://bkslab.org The lab web page] || [[:Category:FAQ|FAQ]] || [[Feedback]] || [[Other tools]] || [[:Category:Problems | Problems]] || [[:Category:Idioms | Idioms]]
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]]  
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|}



Revision as of 20:15, 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

Other Starting Points

Lab members with ssh Databases Molecular Docking Colloidal aggregation Model systems
Hit picking party TLDR Assaying Compound Activity programmatic access (API) Non members without ssh
Software Excipients Aggregator advisor manuals, as they are Systems pharmacology Covalent docking

Organizational pages

Topics Who are you? Idioms Article type Attributes Who are you? Categories Tutorials Problems FAQ

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.