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Welcome to DISI (Disi Is Still Incomplete), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [UCSF | <div id="mainpage"></div><!-- | ||
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Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. It is also a resource for information about our software tools and databases related to ligand discovery, molecular docking and systems pharmacology at the domain "docking.org". We hope you find what you are looking for, but if not, it is editable. Just login and [[contribute | edit it and help us improve]] (please). This wiki aims to serve several [[:Category:Roles | constituencies]], and is a work in progress. [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing] | |||
== | == Popular software and databases == | ||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
! Main article !! Description !! Notes/Links | ! Main article !! Description !! Notes/Links | ||
|- | |- | ||
| [[:Category:DOCK |DOCK]] || Our molecular docking software || Latest are [[DOCK 3. | | [[:Category:DOCK |DOCK]] || Our molecular docking software || Latest are [[DOCK 3.8]] and [[DOCK 6.11]] [https://dock.docking.org dock.docking.org] | ||
|- | |||
| [[:Category:ZINC|ZINC]] || Commercially available compounds || [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22] | |||
|- | |- | ||
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org] | | [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org] | ||
|- | |- | ||
| [[ | | [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate] | ||
|- | |- | ||
| | | [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR] | ||
|- | |- | ||
| [[ | | [[Chemistry commons]] ||Chemistry commons || [https://commons.docking.org TLDR] | ||
|- | |- | ||
| [[ | | [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org] | ||
|} | |} | ||
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|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]] | || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]] | ||
|- | |- | ||
| Techniques || [[Hit picking party]] || [[ | | Techniques || [[Hit picking party]] || [[TLDR]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]] || [[:Category:API | programmatic access (API) ]] | ||
|- | |- | ||
| Enumerations || [[:Category:Software|Software ]] || [[:Category:Databases | Databases]] || [[ | | Enumerations || [[:Category:Software|Software ]] || [[:Category:Databases | Databases]] || [[Excipients]] || [[Aggregator advisor]] || [[Chemistry commons]] | ||
|- | |- | ||
| Navigation || [[:Category:Topic | Topics ]] || [[Special:Categories| Categories]] || [[:Category:Roles |Roles]] | | Navigation || [[:Category:Topic | Topics ]] || [[Special:Categories| Categories]] || [[:Category:Roles |Roles]] | ||
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] | || [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] | ||
|- | |- | ||
| Other || [[:Category:FAQ|FAQ]] || [[Feedback]] || [[ | | Other || [[:Category:FAQ|FAQ]] || [[Feedback]] || [[Other tools]] || xxx || yyy | ||
|} | |} | ||
= 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. | ||
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{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
| Topics || [ | | Topics || [http://www.bkslab.org The lab web page] || yyy | ||
|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]] | || [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]] | ||
|- | |- | ||
| Line 58: | Line 61: | ||
= Support = | = Support = | ||
If you have a problem or a question, we always like to hear about it. | If you have a problem or a question, we always like to hear about it. | ||
[https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing]. More details about ways to communicate with us [[feedback]]. | |||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
| Topics || [ | | Topics || [https://forms.gle/LZV1FCmLWxUWznVi9 Questionnaire] || [[:Category:FAQ|FAQ]] || [[Feedback]] | ||
|| [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]] | |||
|- | |- | ||
| Techniques || [[Hit picking party | | Techniques || [[Hit picking party]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]] || [[:Category:API | programmatic access (API) ]] | ||
|- | |- | ||
| Navigation || [[:Category:Topic | Topics ]] || [[Special:Categories| Categories]] || [[:Category:Roles |Roles]] | | Navigation || [[:Category:Topic | Topics ]] || [[Special:Categories| Categories]] || [[:Category:Roles |Roles]] | ||
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] | || [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] | ||
|- | |- | ||
| | | Information || || || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]] || [[:Category:Theory |Theory pages]] | ||
|} | |} | ||
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[[Category:FAQ]] | [[Category:FAQ]] | ||
[[Category:Public]] | [[Category:Public]] | ||
[[Category:Organization]] | |||
[[Category:Navigation]] | |||
Revision as of 19:12, 26 April 2024
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the Shoichet Lab and Irwin Lab at UCSF. It is also a resource for information about our software tools and databases related to ligand discovery, molecular docking and systems pharmacology at the domain "docking.org". We hope you find what you are looking for, but if not, it is editable. Just login and edit it and help us improve (please). This wiki aims to serve several constituencies, and is a work in progress. Tell us how we are doing
Popular software and databases
| Main article | Description | Notes/Links |
|---|---|---|
| DOCK | Our molecular docking software | Latest are DOCK 3.8 and DOCK 6.11 dock.docking.org |
| ZINC | Commercially available compounds | zinc20 zinc22 |
| SEA | Similarity Ensemble Approach | Drug repurposing, target identification, phenotypic screening. sea.bkslab.org |
| DUDE Family | Benchmarks for docking | dude.docking.org/generate |
| TLDR | TLDR is a Ligand Discovery Resource | TLDR |
| Chemistry commons | Chemistry commons | TLDR |
| DOCK Blaster | A public access service for docking screens | blaster.docking.org |
Other Starting Points
| Topics | Systems pharmacology | Molecular Docking | Colloidal aggregation | Model systems | Covalent docking |
| Techniques | Hit picking party | TLDR | Assaying Compound Activity | Tutorials | programmatic access (API) |
| Enumerations | Software | Databases | Excipients | Aggregator advisor | Chemistry commons |
| Navigation | Topics | Categories | Roles | Article type | Attributes |
| Other | FAQ | Feedback | Other tools | xxx | yyy |
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 | The lab web page | yyy | 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. Tell us how we are doing. More details about ways to communicate with us feedback.
| Topics | Questionnaire | FAQ | Feedback | Model systems | Covalent docking |
| Techniques | Hit picking party | Assaying Compound Activity | Tutorials | programmatic access (API) | |
| Navigation | Topics | Categories | Roles | Article type | Attributes |
| Information | 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.