Main Page

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.