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Welcome to [[DISI:About | DISI]], the site where we document the computer methods in our lab. We invite you to contribute once you create an account and log in to ensure proper attributions. This is not an advertising forum, but if it educates or enlightens, your [[Contribute |contribution]] is welcome.


[[:Category:ZINC|ZINC]] || Commercially available compounds || [http://zinc.docking.org zinc.docking.org]
Welcome to [[DISI:About | DISI]] ("dizzy"), short for DISI Is Still Incomplete), a wiki focusing on molecular docking, ligand discovery tools and computational pharmacology, hosted by docking.org on behalf of the [[Irwin Lab]] and [[Shoichet Lab]] at [[UCSF]].  This wiki aims to serve several [[:Category:Roles | constituencies]], and is a work in progress.  Please [[Contribute |work with us and help us improve]] it.
[https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing]


= What do you want to do? =
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== Ligands for my target ==
* [[:Category:Docking|Molecular Docking]]
* [[:Category:Covalent]]
* [[Hit picking party]] || [[DOCK 3.7]]
* [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest are [[DOCK 3.7]] and [[DOCK 6.6]]
* [[DOCK Blaster]] ||  A public access service for docking screens || [http://blaster.docking.org blaster.docking.org]
* [[DUDE]] and [[DUD]] || Benchmarks for docking|| [http://dude.docking.org/generate dude.docking.org/generate]
* [[HEI]] || Substrate discovery and function ID ||  [http://hei.docking.org hei.docking.org] [http://metabolites.docking.org metabolites.docking.org]


== Targets for my ligand(s) ==
== WHO are you? ==
* [[:Category:Systems pharmacology | Systems pharmacology]]  
This site contains information for lab members and for everyone using our public tools:
* [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID
* [[Welcome group members | Lab members with ssh]]
* [[Welcome web user | Non members without ssh ]]


== Introduction, overview, navigation, help ==  
== WHY are you here? ==
* [[Welcome web user | Welcome! ]]
* [[:Category:Docking | Docking ]] ([[DOCK_3.8|DOCK 3.8]])
* [[Welcome group members | Lab Members]]
* [[:Category:Systems pharmacology | Systems pharmacology]]
* [[:Category:Tutorials | Tutorials ]]
* [[:Category:Aggregation | Colloidal aggregation of small molecules]]
* [[Assaying Compound Activity]]
* [[:Category:Cheminformatics | Chemical informatics]]  
* [[:Category:Topic | Topics ]]
* [[DOCKovalent_3.7]] - Covalent docking
* [[Special:Categories| Categories]]
* more [[:Category:Topic | topics]]
* [[:Category:Roles |Roles]]
* [[:Category:Article type | Article type]]
* [[:Category:Attributes |Attributes]]  
* [[:Category:Software|Software ]]
* [[:Category:Databases | Databases]]
* [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]


== Everything else ==  
== Do you have a question? ==
* [[Group Meeting]] || [http://www.bkslab.org Lab webpages]
We are trying to organize these pages:
*  [[:Category:Aggregation| Colloidal aggregation]]
* [[:Category:Model systems | Model systems ]]
* [[:Category:FAQ|FAQ]] || [[Feedback]]
* [[:Category:Problems | Problems]]
* [[:Category:Theory |Theory pages]]
* [[:Category:Jargon | Jargon]]
[[Aggregator Advisor]] ||A public access database of known aggregators ||  [http://advisor.docking.org advisor.docking.org]


== FOTL ==
* [[:Category:Manual | WHAT ]] - manuals, such as they are.   
* [[Travel Depth]], [[qnifft DOCK 3.6 conversion| QNIFFT]] and [http://crystal.med.upenn.edu/software.html related software] for structural analysis from the [http://crystal.med.upenn.edu/  Sharp lab]
* [[:Category:Tutorials | HOW ]] - Tutorials, such as they are.
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group].
* [[:Category:Theory | WHY ]] - still working on turning our concept into an idea.
* [[Modeller]] - comparative modeling program from the [http://salilab.org Sali Group].
* [[:Category:Article_type | Other ]] - Everything else
* Software vendors: [[OpenEye]], [[ChemAxon]], [[Molinspiration]]
* Software providers: [[rdkit]], [[Knime]]
* [http://zinc.docking.org/browse/catalogs/purchasable.php Compound vendors] and [http://zinc.docking.org/browse/catalogs/annotated.php Annotated catalog providers]
* [[Contract Research Organizations]]
* Transformative databases: [[DrugBank]], [[HMDB]], [[ChEMBL]].


== Still haven't found what you're looking for? ==
Try the search bar top right to see if that works...


[[Category:Info]]
[[Category:Info]]
[[Category:Organization]]

Revision as of 00:24, 26 April 2024

WHO are you?

This site contains information for lab members and for everyone using our public tools:

WHY are you here?

Do you have a question?

We are trying to organize these pages:

  • WHAT - manuals, such as they are.
  • HOW - Tutorials, such as they are.
  • WHY - still working on turning our concept into an idea.
  • Other - Everything else

Still haven't found what you're looking for?

Try the search bar top right to see if that works...

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