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Welcome to [[DISI:About | DISI]], a wiki for computational pharmacology and ligand discovery in the [[Shoichet Lab]] and docking.org.  If you find this site confusing at first, DON'T PANIC!  It has several different purposes and serves several different [[:Category:Roles constituencies]]. Please [[Contribute |work with us and help us improve]] it. If you are new and not a member of the lab, you might try [[Welcome web user]].
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 what's new, please see [[:Category:News | News of changes]]


== So, Why are you here? ==
== Products ==
You may be interested in one of the main research areas of the lab. These are:
{| class="wikitable"
* [[:Category:Docking|Molecular Docking and ligand discovery]]
|-
* [[:Category:Systems pharmacology | Systems pharmacology]]
! Main article !! Description !! Notes/Links
* [[:Category:Aggregation| Colloidal aggregation of small molecules]]
|-
or you may be interested in one of the other [[:Category:Topic | topics]] covered on this wiki.
| [[: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]
|}


== OK, so who are you? ==
== Topics ==
You may prefer to browse this site based on who you are:
{| class="wikitable"
* [[Welcome group members | Lab members, and lab guests with ssh access]]
|-
* [[Welcome web user | Everyone else ]]
| [[: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 ]] || xx
|}


== What sort of question do you have? ==
== Other topics ==
This site is also organized by the types of questions the article aims to answer:
{| 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]]
|}


=== [[:Category:Manual | WHAT ]] ===
== Organizational ==
Manuals for using lab software and tools, descriptions of programs, packages, websites, etc.
{| 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]]
|}


=== [[:Category:Tutorials | HOW ]] ===
Still haven't found what you're looking for? Try the search bar top right to see if that works...
Tutorials and  step-by-step instructions of specific use cases.


=== [[:Category:Theory | WHY ]] ===
= Outages and Support =
Theory and conceptional explanations of techniques. These often not tied to a single program, package, or website and may differ from reality.
We communicate about outages and updates via [https://twitter.com/chem4biology 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


=== [[:Category:Article_type | Other ]] ===
If you have a problem or a question, we always like to hear about it.
Everything else
[https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
More about ways to [[feedback | communicate with us]].
For personalized help, attend [[Weekly office hours]].


== Don't see what you are looking for yet? ==
= Policies, Privacy and all that =  
You may also just use the search bar at the top right to try to find what you are looking for...
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:Info]]
[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Organization]]
[[Category:Navigation]]

Latest revision as of 20:27, 28 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 what's new, please see News of changes

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 xx

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. 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. For personalized help, attend Weekly office hours.

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.

Retrieved from "http://wiki.docking.org/index.php?title=Main_Page&oldid=16106"