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== Are you new here? == | == Are you new here? == | ||
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies. | wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies. | ||
* 1) Molecular docking screens take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). | * 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). | ||
* 2) Analog-by-catalog works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. | * 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. | ||
* 3) Target prediction. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action"). | * 3) '''Target prediction'''. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action"). | ||
We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support. | We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support. | ||
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| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]] | | [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]] | ||
|- | |- | ||
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] || | | [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] || | ||
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Latest revision as of 18:45, 3 December 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. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. Feedback form. News Outages and updates. chat on discord
Are you new here?
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies.
- 1) Molecular docking screens take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]).
- 2) Analog-by-catalog works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties.
- 3) Target prediction. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").
We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.
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 |
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.