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Welcome! We hope you find what you are looking for on this wiki, which is focused on software tools for ligand discovery and systems pharmacology, particularly the tools of the [[Irwin Lab]] and [[Shoichet Lab]] at [[UCSF]].
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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]


{{TOCright}}
== Popular software and databases ==
 
== Software and Databases ==
{| class="wikitable"
{| class="wikitable"
|-
|-
! Main article !! Description !! Notes/Links
! Main article !! Description !! Notes/Links
|-
|-
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest are [[DOCK 3.7]] and [[DOCK 6.7]]
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest are [[DOCK 3.8]] and [[DOCK 6.11]] [https://dock.docking.org dock.docking.org]
|-
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening
| [[:Category:ZINC|ZINC]] || Commercially available compounds || [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
|-
| [[:Category:ZINC|ZINC]] || Commercially available compounds || [http://zinc.docking.org zinc.docking.org]
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
|-
|  [[DOCK Blaster]] || A public access service for docking screens || [http://blaster.docking.org blaster.docking.org]
|  [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
|-
| [[DUDE]] and [[DUD]] || Benchmarks for docking|| [http://dude.docking.org/generate dude.docking.org/generate]
|   [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR]
|-
|-
|  [[Aggregator Advisor]] ||A public access database of known aggregators || [http://advisor.docking.org advisor.docking.org]
|  [[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]
|}
|}


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  || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]]
  || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]]
|-
|-
| Techniques || [[Hit picking party]] || [[DOCK 3.7]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]]  ||  [[:Category:API | programmatic access (API) ]]  
| [[Welcome group members | Lab members with ssh]] || [[Hit picking party]] || [[TLDR]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]]  ||  [[:Category:API | programmatic access (API) ]]  
|-
|-
| Enumerations || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
| [[:Category:Topic | Topics]] || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[Excipients]] || [[Aggregator advisor]] || [[Welcome web user | Non members without ssh ]]
|-
|-
| Navigation || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] ||  [[:Category:Roles |Roles]]  
| [[: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]]
  || [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]]
|-
|-
| Other ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]]  ||  [[:Category:Theory |Theory pages]]
| [https://bkslab.org The lab web page] ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[Other tools]] || [[:Category:Problems | Problems]]  ||  yyy
|}
|}
= Services =
We offer many public [[:Category:Services | services]], including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm.


= Outages =  
Still haven't found what you're looking for? Try the search bar top right to see if that works...
Our servers are up all the time, with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, which is also available as an RSS feed.  We also try to use our Facebook page http://facebook.com/zincdb and our twitter feed [https://twitter.com/chem4biology @chem4biology] when we remember. If there is an unscheduled outage (crash), we will do our best to communicate this via our blog as soon as possible.  If our servers appear down or broken and we have not communicated this, we would be grateful to be told via support at docking.org or +(415) 937-1461
 
= 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


= Support  =
If you have a problem or a question, we always like to hear about it.
If you have a problem or a question, we always like to hear about it. Please see [[feedback]] for how to communicate with us.
[https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
More about ways to [[feedback | communicate with us]].


= Privacy =  
= Policies, Privacy and all that =  
We aim to keep confidential information such as passwords secure, but we can offer no guarantees. You must use these services at your own risk.
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]].
See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc.docking.org available].


[[Category:FAQ]]
[[Category:FAQ]]
[[Category:Public]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Navigation]]

Latest revision as of 20:55, 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=Welcome_web_user&oldid=15737"