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Revision as of 20:47, 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
Lab members with ssh Hit picking party TLDR Assaying Compound Activity Tutorials programmatic access (API)
Topics Software Databases Excipients Aggregator advisor Non members without ssh
WHAT - manuals, such as they are. Topics Categories Roles Article type Attributes
The lab web page 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.