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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 contribution is welcome.
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 contribution is welcome.


[[Welcome web user | NEW USERS]]. [[Welcome group members | LAB MEMBERS]].
{| class="wikitable"
 
|-
[[:Category:DOCK|DOCK]], [[:Category:ZINC|ZINC]], [[:Category:Cheminformatics | Cheminformatics / SEA]],
| [[Welcome web user | NEW USERS]] ||  [[Welcome group members | LAB MEMBERS]] || [[:Category:Portal|Portals]]
[[:Category:DOCK Blaster|Web docking]], [[:Category:Benchmarking | Benchmarking]],
|| [[:Category:Docking|Molecular Docking]] || [[:Category:Cheminformatics|Cheminformatics]] || [[:Category:FAQ|FAQ]] || [[Special:Categories| Categories]]  
[[:Category:Tutorials|Tutorials]], [[:Category:FAQ|FAQ]], [[:Category:Portal|Portals]],
|}
[[Special:Categories| Categories]], [[:Category:Docking|Docking in general]]


= Software and Databases =
= Software and Databases =
{| class="wikitable"
{| class="wikitable"
|-
|-
! Page !! Description !! Notes
! Main article !! Description !! Notes/Links
|-
|-
| [[:Category:DOCK |DOCK]] ||  our molecular docking software ||  the latest versions are [[DOCK 3.7]] and [[DOCK 6.6]]
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest versions: [[DOCK 3.7]] and [[DOCK 6.6]]
|-
|-
| [[SEA]] || the Similarity Ensemble Approach || one application of which is drug repurposing
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID
|-
|-
|  [[:Category:ZINC|ZINC]] || A public access database of commercially available compounds for screening. || ZINC
|  [[:Category:ZINC|ZINC]] || A public access database of commercially available compounds || [http://zinc.docking.org zinc.docking.org]
|-
|-
|  [[DOCK Blaster]] ||  A public access service for running docking screens. || DOCK Blaster
|  [[DOCK Blaster]] ||  A public access service for docking screens || [http://blaster.docking.org blaster.docking.org]
|-
|-
|  [[DUDE]] and [[DUD]] ||A Directory of Useful Decoys for benchmarking docking programs. ||  Decoys
|  [[DUDE]] and [[DUD]] || Docking benchmarks || [http://dude.docking.org/generate dude.docking.org/generate]
|-
|-
|  [[HEI]] || High energy intermediates for substrate discovery and function identification ||  HEI
|  [[HEI]] || High energy intermediates for substrate discovery and function identification ||  [http://hei.docking.org hei.docking.org] [http://metabolites.docking.org metabolites.docking.org]
|-
|-
|  [[Aggregator Advisor]] ||A public access database of known aggregators ||  Aggregation
|  [[Aggregator Advisor]] ||A public access database of known aggregators ||  [http://advisor.docking.org advisor.docking.org]
|-
|  [[DUDE]] and [[DUD]] ||A Directory of Useful Decoys for benchmarking docking programs. ||  Decoys
|}
|}
 
== Software by 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]


[[Category:Portal]]
[[Category:Portal]]

Revision as of 00:43, 11 March 2014

Welcome to DISI (DISI Is Still Incomplete), documentation of 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.

NEW USERS LAB MEMBERS Portals Molecular Docking Cheminformatics FAQ Categories

Software and Databases

Main article Description Notes/Links
DOCK Our molecular docking software Latest versions: 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 Docking benchmarks dude.docking.org/generate
HEI High energy intermediates for substrate discovery and function identification hei.docking.org metabolites.docking.org
Aggregator Advisor A public access database of known aggregators advisor.docking.org

Software by friends of the lab

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