Welcome web user: Difference between revisions

From DISI
Jump to navigation Jump to search
mNo edit summary
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
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 [[Irwin Lab]] and [[Shoichet Lab]] at [[UCSF]].
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 ==
== Software and Databases ==
Line 6: Line 6:
! Main article !! Description !! Notes/Links
! Main article !! Description !! Notes/Links
|-
|-
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest are [[DOCK 3.7]] and [[DOCK 6.7]]
| [[: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. [http://sea.bkslab.org/ sea.bkslab.org]
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
|-
|  [[:Category:ZINC|ZINC]] || Commercially available compounds || [http://zinc15.docking.org zinc15.docking.org]
|  [[:Category:ZINC|ZINC]] || Commercially available compounds || [https://zinc15.docking.org zinc15.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 || [https://blaster.docking.org blaster.docking.org]
|-
|-
|  [[DUDE]] and [[DUD]] || Benchmarks for docking|| [http://dude.docking.org/generate dude.docking.org/generate]
|  [[DUDE]] and [[DUD]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
|-
|  [[Aggregator Advisor]] ||A public access database of known aggregators ||  [http://advisor.docking.org advisor.docking.org]
|  [[TLDR]] ||TLDR is a Ligand Discovery Resource ||  [https://tldr.docking.org advisor.docking.org]
|-
| [[Other_tools]] || Other tools and databases ||  link goes here
|}
|}


Line 36: Line 38:
= 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.
{| 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]]
|}


= Outages =  
= Outages =  
Line 43: Line 60:
If you have a problem or a question, we always like to hear about it. Please see [[feedback]] for how to communicate with us.
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 =  
{| 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]]
|}
 
= 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.
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].
See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc15.docking.org available].

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"