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! Main article !! Description !! Notes/Links | ! Main article !! Description !! Notes/Links | ||
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| [[:Category:DOCK |DOCK]] || Our molecular docking software || Latest | | [[:Category:DOCK |DOCK]] || Our molecular docking software || Latest are [[DOCK 3.7]] and [[DOCK 6.6]] | ||
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| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID | | [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID | ||
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| [[Aggregator Advisor]] ||A public access database of known aggregators || [http://advisor.docking.org advisor.docking.org] | | [[Aggregator Advisor]] ||A public access database of known aggregators || [http://advisor.docking.org advisor.docking.org] | ||
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== Friends of the lab == | == Friends of the lab == | ||
* [[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] | * [[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] | ||
Revision as of 15:00, 21 March 2014
Welcome to DISI, a wiki to document the software, databases and methods of the Shoichet Lab and the fields of molecular docking and cheminformatics. We invite you to contribute once you create an account and log in to ensure proper attributions. Eligible topics include both free and commercial software, databases, papers and methods. This is not an advertising forum, but if it educates or enlightens, your contribution is welcome.
Starting Points
Software and Databases
| Main article | Description | Notes/Links |
|---|---|---|
| DOCK | Our molecular docking software | Latest are DOCK 3.7 and DOCK 6.6 |
| SEA | Similarity Ensemble Approach | Drug repurposing, target ID |
| ZINC | A public access database of commercially available compounds | zinc.docking.org |
| DOCK Blaster | A public access service for docking screens | blaster.docking.org |
| DUDE and DUD | Benchmarks for docking | dude.docking.org/generate |
| HEI | Substrate discovery and function ID | hei.docking.org metabolites.docking.org |
| Aggregator Advisor | A public access database of known aggregators | advisor.docking.org |
Friends of the lab
- Travel Depth, QNIFFT and related software for structural analysis from the Sharp lab
- PLOP - protein modeling program from the Jacobson group.
- Modeller - comparative modeling program from the Sali Group.
- Software vendors: OpenEye, ChemAxon, Molinspiration
- Software providers: rdkit, Knime
- Compound vendors and Annotated catalog providers
- Transformative databases: DrugBank, HMDB, ChEMBL.