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Welcome to our web pages. We hope you like them.
Welcome to DISI (Disi Is Still Incomplete), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [UCSF | the University of California San Francisco]. It is also a resource for software tools and databases related to ligand discovery and pharmacology "docking.org".  We hope you find what you are looking for, but if not, it is editable. If you don't like it, login and change it (please).


== 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]] [https://dock.docking.org dock.docking.org]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
|  [[:Category:ZINC|ZINC]] || Commercially available compounds || [https://zinc15.docking.org zinc15.docking.org]
|-
|  [[DOCK Blaster]] ||  A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|-
|  [[DUDE]] and [[DUD]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
|  [[TLDR]] ||TLDR is a Ligand Discovery Resource ||  [https://tldr.docking.org advisor.docking.org]
|-
| [[Other_tools]] || Other tools and databases ||  link goes here
|}
== 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 services, including software and databases that are free to download. For software downloads, for-profit organizations are generally required to pay.
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.
 
{| 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]]
|}


* [http://dock.compbio.ucsf.edu DOCK] molecular docking software.  
= Outages =
* [[ZINC]] database of commercially available compounds for ligand discovery and virtual screening.  
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
* [[SEA]] - similarity ensemble approach for predicting the biological targets of small molecules
* [[DOCK Blaster]] - free molecular docking website
* [[DUD]] and [[DUDE]] benchmarking databases for assessing molecular docking performance.  
* [[Aggregator Advisor]] - all about small molecule colloidal aggregation and how to avoid it.
* [http://www.bkslab.org | The lab web page]] including publications and information about lab members.
* This wiki, which contains documentation to which you may contribute.  


{{TOCright}}
= Support  =
= Maintenance and Outages =  
If you have a problem or a question, we always like to hear about it. Please see [[feedback]] for how to communicate with us.
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 and our twitter feed [https://twitter.com/chem4biology @chem4biology].  If there is an unscheduled outage, we will do our best to communicate this via twitter and the 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 =
{| class="wikitable"
If you have a problem or a question, we always like to hear about it. Please write on our blog http://docking.org or our facebook page http://facebook.com/zincdb where we or a member of the community will answer if we can.
|-
| 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]]
|}


= Privacy and Security =  
= Policies, Privacy and all that =  
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://zinc15.docking.org available].


[[Category:Tutorials]]
[[Category:FAQ]]
[[Category:Public]]

Revision as of 20:01, 24 April 2024

Welcome to DISI (Disi Is Still Incomplete), the wiki of the Shoichet Lab and Irwin Lab at [UCSF | the University of California San Francisco]. It is also a resource for software tools and databases related to ligand discovery and pharmacology "docking.org". We hope you find what you are looking for, but if not, it is editable. If you don't like it, login and change it (please).

Software and Databases

Main article Description Notes/Links
DOCK Our molecular docking software Latest are DOCK 3.7 and DOCK 6.7 dock.docking.org
SEA Similarity Ensemble Approach Drug repurposing, target identification, phenotypic screening. sea.bkslab.org
ZINC Commercially available compounds zinc15.docking.org
DOCK Blaster A public access service for docking screens blaster.docking.org
DUDE and DUD Benchmarks for docking dude.docking.org/generate
TLDR TLDR is a Ligand Discovery Resource advisor.docking.org
Other_tools Other tools and databases link goes here

Other Starting Points

Topics Systems pharmacology Molecular Docking Colloidal aggregation Model systems Covalent docking
Techniques Hit picking party DOCK 3.7 Assaying Compound Activity Tutorials programmatic access (API)
Enumerations Software Databases Free Free to some Commercial
Navigation Topics Categories Roles Article type Attributes
Other FAQ Feedback Problems Jargon Theory pages

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.

Topics Systems pharmacology Molecular Docking Colloidal aggregation Model systems Covalent docking
Techniques Hit picking party DOCK 3.7 Assaying Compound Activity Tutorials programmatic access (API)
Enumerations Software Databases Free Free to some Commercial
Navigation Topics Categories Roles Article type Attributes
Other FAQ Feedback Problems Jargon Theory pages

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.

Topics Systems pharmacology Molecular Docking Colloidal aggregation Model systems Covalent docking
Techniques Hit picking party DOCK 3.7 Assaying Compound Activity Tutorials programmatic access (API)
Enumerations Software Databases Free Free to some Commercial
Navigation Topics Categories Roles Article type Attributes
Other FAQ Feedback Problems Jargon Theory pages

Policies, Privacy and all that

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.

Retrieved from "http://wiki.docking.org/index.php?title=Welcome_web_user&oldid=15689"