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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]].
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]].  It is also a resource for information about our software tools and databases related to ligand discovery, molecular docking and systems pharmacology 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]], and is a work in progress. [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing]


== So, Why are you here? ==
== Popular software and databases ==
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 ||  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]
|-
| [[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 TLDR]
|-
| [[DOCK Blaster]] ||  A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|}


== OK, so who are you? ==
== Other Starting Points ==
Or, you may prefer to browse based on who you are:
{| class="wikitable"
* [[Welcome group members | Lab Members and colleagues]]
|-
* [[Welcome web user | Everyone else ]]
| Topics ||  [[:Category:Systems pharmacology | Systems pharmacology]]  ||  [[:Category:Docking|Molecular Docking]]
|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]]
|-
| [[Welcome group members | Lab members with ssh]] || [[Hit picking party]] || [[TLDR]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]]  ||  [[:Category:API | programmatic access (API) ]]
|-
| [[:Category:Topic | Topics]] || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[Excipients]] || [[Aggregator advisor]] || [[Welcome web user | Non members without ssh ]]
|-
| [[:Category:Manual | WHAT ]] - manuals, such as they are.  || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] ||  [[:Category:Roles |Roles]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]]
|-
| [https://bkslab.org The lab web page] ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[Other tools]] || [[:Category:Problems | Problems]]  ||  yyy
|}


== Type of Article ==
Still haven't found what you're looking for? Try the search bar top right to see if that works...
This site is also organized by the types of questions the articles aim to answer:
* [[:Category:Manual | WHAT ]] - descriptions of programs, packages, websites
* [[:Category:Tutorials | HOW ]] - step-by-step instructions, ideally
* [[:Category:Theory | WHY ]] - explanations, often not tied to a single program, package, or website.
* [[:Category:Article_type | Other ]] - everything else


You may also just use the search bar at the top left to try to find what you are looking for...
= Outages and Support =
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:Info]]
If you have a problem or a question, we always like to hear about it.
[https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
More about ways to [[feedback | 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 [[DISI:Privacy_policy|privacy policy]].
 
[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Organization]]
[[Category:Navigation]]

Latest revision as of 20:56, 26 April 2024

Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the Shoichet Lab and Irwin Lab at UCSF. It is also a resource for information about our software tools and databases related to ligand discovery, molecular docking and systems pharmacology 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, and is a work in progress. Tell us how we are doing

Popular software and databases

Main article Description Notes/Links
DOCK Our molecular docking software Latest are DOCK 3.8 and DOCK 6.11 dock.docking.org
ZINC Commercially available compounds 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 TLDR
DOCK Blaster A public access service for docking screens blaster.docking.org

Other Starting Points

Topics Systems pharmacology Molecular Docking Colloidal aggregation Model systems Covalent docking
Lab members with ssh Hit picking party TLDR Assaying Compound Activity Tutorials programmatic access (API)
Topics Software Databases Excipients Aggregator advisor Non members without ssh
WHAT - manuals, such as they are. Topics Categories Roles Article type Attributes
The lab web page FAQ Feedback Other tools Problems yyy

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.

Retrieved from "http://wiki.docking.org/index.php?title=Main_Page&oldid=15738"