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Welcome to DISI (DISI Is Still Incomplete), documentation of the software, databases and methods of the [[Shoichet Lab]] and the fields of [[:Category:Docking | molecular docking]] and [[:Category:Cheminformatics | cheminformatics]].  We invite you to contribute once you create an account and log in to ensure proper attributions.  Eligible topics include both [[: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: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.


== Starting Points ==
== Starting Points ==
{| class="wikitable"
{| class="wikitable"
|-
|-
| [[Welcome web user | Welcome! ]] ||  [[Welcome group members | Lab Members]] / [[Group Meeting]]
| [[Welcome web user | Welcome! ]] ||  [[Welcome group members | Lab Members]] ||  [[Group Meeting]] || [http://www.bkslab.org Lab webpages]  
|| [[:Category:Docking|Molecular Docking]] || [[:Category:Cheminformatics|Cheminformatics / SEA]]
|-
|-
| [http://www.bkslab.org Lab webpage] ||  [[:Category:Tutorials | Tutorials ]] || [[:Category:Theory |Theory pages]] || [[:Category:Jargon | Jargon]]  
| [[:Category:Systems pharmacology | Systems pharmacology]] ||  [[:Category:Docking|Molecular Docking]]
|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent]]
|-
|-
| [[:Category:Portal|Portals]]  || [[Special:Categories| Categories]]
| [[:Category:Tutorials | Tutorials ]] || [[Hit picking party]] || [[DOCK 3.7]] || [[Assaying Compound Activity]]
|| [[Hit picking party]] || [[:Category:Article type | Article type]] / [[:Category:Topic | Topic ]]
|-
|  [[: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:FAQ|FAQ]] || [[Feedback]]  / [[:Category:Problems | Problems]]  
|| [[:Category:Roles |Roles]] || [[DOCK 3.7]]  
|| [[:Category:Theory |Theory pages]] || [[:Category:Jargon | Jargon]]  
|-
|-
| [[:Category:Software|Software : ]] || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
| [[:Category:Software|Software ]] / [[:Category:Databases | Databases]] -> || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
|}
|}


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! Main article !! Description !! Notes/Links
! Main article !! Description !! Notes/Links
|-
|-
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest versions: [[DOCK 3.7]] and [[DOCK 6.6]]
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest are [[DOCK 3.7]] and [[DOCK 6.6]]
|-
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID
|-
|-
|  [[:Category:ZINC|ZINC]] || A public access database of commercially available compounds || [http://zinc.docking.org zinc.docking.org]
|  [[: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]
|  [[DOCK Blaster]] ||  A public access service for docking screens || [http://blaster.docking.org blaster.docking.org]
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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]
|}
|}
== 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]
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group].
* [[PLOP]] - protein modeling program from the [http://francisco.compbio.ucsf.edu/~jacobson/ Jacobson group].
* [[Modeler]] - comparative modeling program from the [http://salilab.org Sali Group].  
* [[Modeller]] - comparative modeling program from the [http://salilab.org Sali Group].  
* Software vendors: [[OpenEye]], [[ChemAxon]], [[Molinspiration]]
* Software vendors: [[OpenEye]], [[ChemAxon]], [[Molinspiration]]
* Software providers: [[rdkit]], [[Knime]]
* 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]
* [http://zinc.docking.org/browse/catalogs/purchasable.php Compound vendors] and [http://zinc.docking.org/browse/catalogs/annotated.php Annotated catalog providers]
* Particular databases: [[Drugbank]], [[HMDB]], [[ChEMBL]].
* [[Contract Research Organizations]]
* Transformative databases: [[DrugBank]], [[HMDB]], [[ChEMBL]].




[[Category:Info]]
[[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

Welcome! Lab Members Group Meeting Lab webpages
Systems pharmacology Molecular Docking Colloidal aggregation Model systems Category:Covalent
Tutorials Hit picking party DOCK 3.7 Assaying Compound Activity
Topics Categories Roles Article type / Attributes
FAQ Feedback / Problems Theory pages Jargon
Software / Databases -> Free Free to some Commercial

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