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Welcome to [[DISI:About | DISI]], a wiki for computational pharmacology and ligand discovery. If you find this site confusing at first, DON'T PANIC!  It has several different purposes and aims to serve several different constituencies.  Please [[Contribute |work with us and help us improve]] it. Should you prefer the OLD MAIN PAGE, it is [[Old_Main | still available]]. Also, the [[Welcome web user]] page looks a lot like the old main page.
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". To contribute, login and [[contribute | edit to help us improve]] (please!). This wiki serves several [[:Category:Roles | constituencies]].


== So, Why are you here? ==
[https://forms.gle/LZV1FCmLWxUWznVi9 Feedback form]. [[:Category:News | News]] [https://x.com/chem4biology/ Outages and updates]. [https://discord.gg/4MpD6UF5AN chat on discord]
You may be interested in one of the main research areas of the lab. These are:
* [[:Category:Docking|Molecular Docking and ligand discovery]]
* [[:Category:Systems pharmacology | Systems pharmacology]]
* [[:Category:Aggregation| Colloidal aggregation of small molecules]]
or you may be interested in one of the other [[:Category:Topic | topics]] covered on this wiki.


== OK, so who are you? ==
== Products ==
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 ]]
! 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]
|}


== Type of Article ==
== Topics ==
This site is also organized by the types of questions the article aims to answer:
{| 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 ]] || xx
|}


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


=== [[: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.


= 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) 937-1461
* [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.


=== [[:Category:Theory | WHY ]] ===
= 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]].


Theory and conceptional explanations of techniques. These often not tied to a single program, package, or website and may differ from reality.
[[Category:FAQ]]
 
[[Category:Public]]
 
=== [[:Category:Article_type | Other ]] ===
Everything else
 
You may also just use the search bar at the top right to try to find what you are looking for...
 
[[Category:Info]]
[[Category:Organization]]
[[Category:Organization]]
[[Category:Navigation]]

Latest revision as of 19:36, 14 November 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". To contribute, login and edit to help us improve (please!). This wiki serves several constituencies.

Feedback form. News Outages and updates. chat on discord

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.
  • 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) 937-1461
  • 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.

Retrieved from "http://wiki.docking.org/index.php?title=Main_Page&oldid=16413"