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Welcome | Welcome! We hope you find what you are looking for on this wiki, which is focused on software tools for ligand discovery and systems pharmacology, particularly the tools of the [[Shoichet Lab]] at [[UCSF]]. | ||
{{TOCright}} | |||
== Software and Databases == | |||
{| class="wikitable" | |||
|- | |||
! Main article !! Description !! Notes/Links | |||
|- | |||
| [[:Category:DOCK |DOCK]] || Our molecular docking software || Latest are [[DOCK 3.7]] and [[DOCK 6.7]] | |||
|- | |||
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening | |||
|- | |||
| [[: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] | |||
|- | |||
| [[Aggregator Advisor]] ||A public access database of known aggregators || [http://advisor.docking.org advisor.docking.org] | |||
|} | |||
== Other Starting Points == | |||
{| class="wikitable" | |||
|- | |||
| Topics || [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Docking|Molecular Docking]] | |||
|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]] | |||
|- | |||
| Techniques || [[Hit picking party]] || [[DOCK 3.7]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]] || [[:Category:API | programmatic access (API) ]] | |||
|- | |||
| Enumerations || [[:Category:Software|Software ]] || [[:Category:Databases | Databases]] || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]] | |||
|- | |||
| Navigation || [[:Category:Topic | Topics ]] || [[Special:Categories| Categories]] || [[:Category:Roles |Roles]] | |||
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] | |||
|- | |||
| Other || [[:Category:FAQ|FAQ]] || [[Feedback]] || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]] || [[:Category:Theory |Theory pages]] | |||
|} | |||
= Services = | = Services = | ||
We offer many public [[:Category:Services | services]], including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm. | We offer many public [[:Category:Services | services]], including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm. | ||
= Outages = | = Outages = | ||
Our servers are up all the time with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, Facebook page http://facebook.com/zincdb and our twitter feed [https://twitter.com/chem4biology @chem4biology]. If there is an unscheduled outage (crash), we will do our best to communicate this via | Our servers are up all the time, with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, which is also available as an RSS feed. We also try to use our Facebook page http://facebook.com/zincdb and our twitter feed [https://twitter.com/chem4biology @chem4biology] when we remember. If there is an unscheduled outage (crash), we will do our best to communicate this via our blog as soon as possible. If our servers appear down or broken and we have not communicated this, we would be grateful to be told via support at docking.org or +(415) 937-1461 | ||
= Support = | = Support = | ||
| Line 15: | Line 46: | ||
= Privacy = | = Privacy = | ||
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. | We aim to keep confidential information such as passwords secure, but we can offer no guarantees. You must use these services at your own risk. | ||
See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc.docking.org available]. | See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc.docking.org available]. | ||
[[Category:FAQ]] | [[Category:FAQ]] | ||
[[Category:Roles]] | [[Category:Roles]] | ||
Revision as of 05:10, 3 June 2015
Welcome! We hope you find what you are looking for on this wiki, which is focused on software tools for ligand discovery and systems pharmacology, particularly the tools of the Shoichet Lab at UCSF.
Software and Databases
| Main article | Description | Notes/Links |
|---|---|---|
| DOCK | Our molecular docking software | Latest are DOCK 3.7 and DOCK 6.7 |
| SEA | Similarity Ensemble Approach | Drug repurposing, target identification, phenotypic screening |
| 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 |
| Aggregator Advisor | A public access database of known aggregators | advisor.docking.org |
Other Starting Points
Services
We offer many public services, including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm.
Outages
Our servers are up all the time, with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, which is also available as an RSS feed. We also try to use our Facebook page http://facebook.com/zincdb and our twitter feed @chem4biology when we remember. If there is an unscheduled outage (crash), we will do our best to communicate this via our blog as soon as possible. If our servers appear down or broken and we have not communicated this, we would be grateful to be told via support at docking.org or +(415) 937-1461
Support
If you have a problem or a question, we always like to hear about it. Please see feedback for how to communicate with us.
Privacy
We aim to keep confidential information such as passwords secure, but we can offer no guarantees. You must use these services at your own risk. See our privacy policy. An SSL version of ZINC is available.