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Welcome to | Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". To contribute, login and [[contribute | edit to help us improve]] (please!). This wiki serves several [[:Category:Roles | constituencies]]. | ||
[https://forms.gle/LZV1FCmLWxUWznVi9 Feedback form]. [[:Category:News | News]] [https://x.com/chem4biology/ Outages and updates]. [https://discord.gg/4MpD6UF5AN chat on discord] | |||
== | == Products == | ||
{| class="wikitable" | |||
|- | |||
! Main article !! Description !! Notes/Links | |||
|- | |||
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org] | |||
|- | |||
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [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] | |||
|- | |||
| [[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 Chemistry Commons] | |||
|- | |||
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org] | |||
|} | |||
== | == Topics == | ||
{| class="wikitable" | |||
|- | |||
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]] | |||
|| [[Hit picking party]] | |||
|- | |||
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]] | |||
|- | |||
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] || xx | |||
|} | |||
== Other topics == | |||
{| class="wikitable" | |||
|- | |||
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]] | |||
|- | |||
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]] | |||
|- | |||
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]] | |||
|} | |||
== | == Organizational == | ||
{| class="wikitable" | |||
|- | |||
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]] | |||
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]] | |||
|- | |||
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]] | |||
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]] | |||
|} | |||
[[Category: | Still haven't found what you're looking for? Try the search bar top right to see if that works... | ||
= Outages and Support = | |||
* We communicate about outages and updates via [https://twitter.com/chem4biology X]. | |||
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server] | |||
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461 | |||
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing]. | |||
* More about ways to [[feedback | communicate with us]]. | |||
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free. | |||
= 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. See our [[DISI:Privacy_policy|privacy policy]]. | |||
[[Category:FAQ]] | |||
[[Category:Public]] | |||
[[Category:Organization]] | [[Category:Organization]] | ||
[[Category:Navigation]] | |||
Latest revision as of 19:36, 14 November 2024
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the Shoichet Lab and Irwin Lab at UCSF. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". To contribute, login and edit to help us improve (please!). This wiki serves several constituencies.
Feedback form. News Outages and updates. chat on discord
Products
| Main article | Description | Notes/Links |
|---|---|---|
| DOCK | Our molecular docking software | There are two main branches. The latest are DOCK 3.8 and DOCK 6.11 dock.docking.org |
| ZINC | Commercially available compounds | There are two databases 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 | Chemistry Commons |
| DOCK Blaster | A public access service for docking screens | blaster.docking.org |
Topics
| Databases | Molecular Docking | Colloidal aggregation | Hit picking party |
| Systems pharmacology | Covalent docking | Chemical Space | Decoys |
| Fragment Docking | Excipients | Model systems | xx |
Other topics
| Lab members with ssh | Non members without ssh | Assaying Compound Activity |
| Run on our servers | Run on your servers | Set up a lab |
| programmatic access (API) | Software | Aggregator advisor |
Organizational
| Topics | Who are you? | Idioms | Article type | Attributes | Policies |
| Categories | Tutorials | Problems | FAQ | Manuals | Jargon |
Still haven't found what you're looking for? Try the search bar top right to see if that works...
Outages and Support
- We communicate about outages and updates via X.
- We have open conversations among ourselves and with users on our discord server. discord server
- If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461
- Tell us how we are doing.
- More about ways to communicate with us.
- Weekly office hours. 11 am PT is the 'daily' office hours on discord, if we are free.
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. See our privacy policy.