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--> __NOTOC__ | Welcome to [[DISI:About | DISI]], documentation of the software, databases and methods of the [[Shoichet Lab]] and the fields of [[:Category:Docking | molecular docking]] and [[:Category:Cheminformatics | cheminformatics]] for [[systems pharmacology]]. We invite you to contribute once you create an account and log in to ensure proper attributions. Eligible topics include [[:Category:free | free]] and [[:Category:commercial | commercial]] [[:Category:software | software]], [[:Category:databases | databases]], [[:Category:papers | papers]] and [[:Category:Tutorials | methods]]. This is not an advertising forum, but if it educates or enlightens, your [[Contribute |contribution]] is welcome. | ||
Welcome to DISI | |||
== Starting Points == | |||
{| class="wikitable" | |||
|- | |||
| [[Welcome web user | Welcome! ]] || [[Welcome group members | Lab Members]] || [[Group Meeting]] || [http://www.bkslab.org Lab webpages] | |||
|- | |||
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Docking|Molecular Docking]] | |||
|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent]] | |||
|- | |||
| [[:Category:Tutorials | Tutorials ]] || [[Hit picking party]] || [[DOCK 3.7]] || [[Assaying Compound Activity]] | |||
|- | |||
| [[:Category:Topic | Topics ]] || [[Special:Categories| Categories]] | |||
|| [[:Category:Roles |Roles]] || [[:Category:Article type | Article type]] / [[:Category:Attributes |Attributes]] | |||
|- | |||
| [[:Category:FAQ|FAQ]] || [[Feedback]] / [[:Category:Problems | Problems]] | |||
|| [[:Category:Theory |Theory pages]] || [[:Category:Jargon | Jargon]] | |||
|- | |||
| [[:Category:Software|Software ]] / [[:Category:Databases | Databases]] -> || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]] | |||
|} | |||
[[ | == Software and Databases == | ||
{| class="wikitable" | |||
|- | |||
! Main article !! Description !! Notes/Links | |||
|- | |||
| [[:Category:DOCK |DOCK]] || Our molecular docking software || Latest are [[DOCK 3.7]] and [[DOCK 6.6]] | |||
|- | |||
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID | |||
|- | |||
| [[:Category:ZINC|ZINC]] || Commercially available compounds || [http://zinc.docking.org zinc.docking.org] | |||
|- | |||
| [[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] | |||
|- | |||
| [[Aggregator Advisor]] ||A public access database of known aggregators || [http://advisor.docking.org advisor.docking.org] | |||
|} | |||
= | == 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] | ||
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group]. | |||
* [[Modeller]] - comparative modeling program from the [http://salilab.org Sali Group]. | |||
* 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]]. | |||
[[Category: | [[Category:Info]] | ||
Latest revision as of 05:11, 3 June 2015
Welcome to DISI, documentation of the software, databases and methods of the Shoichet Lab and the fields of molecular docking and cheminformatics for systems pharmacology. We invite you to contribute once you create an account and log in to ensure proper attributions. Eligible topics include 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 | 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
- Contract Research Organizations
- Transformative databases: DrugBank, HMDB, ChEMBL.