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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 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]
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== Software and Databases ==
This wiki contains information for both members of the lab as well as the general public.
{| class="wikitable"
If you have arrived here, you have identified as not being a member of our lab.  
|-
That's ok, there is still lots of ways we can help you.  
! Main article !! Description !! Notes/Links
Many of our services and databases are available on the web.
|-
| [[: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. [https://sea.bkslab.org/ sea.bkslab.org]
|-
|  [[:Category:ZINC|ZINC]] || Commercially available compounds || [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
|  [[DOCK Blaster]] ||  A public access service for docking screens || [https://blaster.docking.org blaster.docking.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]
|-
| [[Other_tools]] || Other tools and databases ||  link goes here
|}


== Other Starting Points ==
Here is the model.
{| class="wikitable"
We have software that runs on our website.
|-
We have software that you can download and run on your own computer.  
| Topics ||  [[:Category:Systems pharmacology | Systems pharmacology]]  ||  [[:Category:Docking|Molecular Docking]]
We also have software that can be run in the cloud.  
|| [[: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) ]]
|-
| Enumerations || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
|-
| Navigation || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] ||  [[:Category:Roles |Roles]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]]
|-
| Other ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]]  ||  [[:Category:Theory |Theory pages]]
|}
= 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.


{| class="wikitable"
All of our databases can be downloaded and hosted locally on your server. For example, [[ZINC20]] and [[ZINC22]].  
|-
Our web interface to run software on our cluster is [[TLDR]]. Of course, since you are using our cluster, it won't be as fast as if you had it installed locally on your own system.
| Topics ||  [[:Category:Systems pharmacology | Systems pharmacology]] ||  [[:Category:Docking|Molecular 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) ]]
|-
| Enumerations || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
|-
| Navigation || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] || [[:Category:Roles |Roles]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]]
|-
| Other ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]]  ||  [[:Category:Theory |Theory pages]]
|}


= Outages =  
== What can I not do if I am not a member of the lab ==  
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
* You cannot ssh in to our computers (but we have lots of free public websites!)
* you cannot run software on the command line (but we have TLDR and other websites that allow you to run software on our hardware
* you cannot access various services that are private to UCSF and/or the lab


= Support  =
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]
Please see [[feedback]] for how to communicate with us.
{| class="wikitable"
|-
| Topics ||  [[:Category:Systems pharmacology | Systems pharmacology]]  ||  [[:Category:Docking|Molecular 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) ]]
|-
| Enumerations || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
|-
| Navigation || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] ||  [[:Category:Roles |Roles]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]]
|-
| Other ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]]  ||  [[:Category:Theory |Theory pages]]
|}
= 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.
See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc15.docking.org available].


[[Category:FAQ]]
[[Category:FAQ]]
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[[Category:Organization]]
[[Category:Organization]]
[[Category:Navigation]]
[[Category:Navigation]]
[[Category:Needs work]]

Latest revision as of 23:25, 31 May 2024

This wiki contains information for both members of the lab as well as the general public. If you have arrived here, you have identified as not being a member of our lab. That's ok, there is still lots of ways we can help you. Many of our services and databases are available on the web.

Here is the model. We have software that runs on our website. We have software that you can download and run on your own computer. We also have software that can be run in the cloud.

All of our databases can be downloaded and hosted locally on your server. For example, ZINC20 and ZINC22. Our web interface to run software on our cluster is TLDR. Of course, since you are using our cluster, it won't be as fast as if you had it installed locally on your own system.

What can I not do if I am not a member of the lab

  • You cannot ssh in to our computers (but we have lots of free public websites!)
  • you cannot run software on the command line (but we have TLDR and other websites that allow you to run software on our hardware
  • you cannot access various services that are private to UCSF and/or the lab
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