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Welcome! We hope you find what you are looking for on this wiki, which is focused on software tools for ligand discovery and systems pharmacology, particularly the tools of the Irwin Lab and Shoichet Lab at UCSF.

Software and Databases

Main article Description Notes/Links
DOCK Our molecular docking software Latest are DOCK 3.7 and DOCK 6.7
SEA Similarity Ensemble Approach Drug repurposing, target identification, phenotypic screening. sea.bkslab.org
ZINC Commercially available compounds zinc15.docking.org
DOCK Blaster A public access service for docking screens blaster.docking.org
DUDE and DUD Benchmarks for docking dude.docking.org/generate
Aggregator Advisor A public access database of known aggregators advisor.docking.org

Other Starting Points

Topics Systems pharmacology Molecular Docking 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


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.


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


If you have a problem or a question, we always like to hear about it. Please see feedback for how to communicate with us.


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.