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Discuss all software and databases at docking.org, including: ZINC, DOCK, DOCK Blaster, SEA, DUD, HEI, Aggregator Advisor, THC, WINC, DISI and this blog itself. http://docking.org
Discuss the ZINC 12 interface. Topics include how to use, browser compatibility, current limitations, forming complex queries, command language, the shopping cart, creating decoys, uploading molecules, purchasing-related features, bugs and feature requests. Reports of successes and tales of woe from the trenches. http://zinc.docking.org.
14291 year 3 weeks ago
by John Irwin
Forum for discussion of the contents of the ZINC database. Topics include which vendors and catalogs are included, correctness of / problems with representations, subsets, problematic or broken molecules, incorrect tautomers or protonation states, molecular conformation, partial atomic charges, desolvation, unlikely torsion angles. Also: successes and failures with purchasing, suggested vendors to include, problems with individual subsets, definitions of by-property and special subsets. Reports of successes and tales of woe from the trenches. http://zinc.docking.org
284836 weeks 4 days ago
by samdani
Forum for the discussion of all aspects of the use of DOCK 6. Topics include: installation, operating system related issues, tests, benchmarks. http://dock.docking.org
472 years 19 weeks ago
by Syeda Sumayya Tariq
Forum for the discussion of DOCK Blaster. Topics include use of PDB files, comparative models, pocket picking (with CLIPPERS), downloading results to continue calculations on your local computer, how to evaluate if docking is working, hit picking parties. Bug reports and feature requests. Reports of successes and tales of woe from the trenches. http://blaster.docking.org.
114 years 1 week ago
by Roger Williams
Discussion of aggregation, aggregators and the aggregator advisor. Topics include: methods to determine aggregation, methods to predict aggregation, reports of aggregation. http://advisor.docking.org
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Forum for the discussion of decoys, enrichment, and how to measure docking performance. Topics include: docking metrics, directory of useful decoys (DUD), benchmarking, decoys. http://dud.docking.org
241 year 27 weeks ago
by Johnmario
Talk about things.
Discussion about vendor databases (e.g. new sources not in ZINC) and annotated catalogs of molecular bioactivity information.
71448 weeks 6 days ago
by damjanmk
Forum for the discussion of both ground state and high energy intermediates (HEI) in docking for the purpose of protein function prediction. Topic includes: half reactions, covalent docking, metalloenzymes, predictions, collaborations, strategies and methods. http://hei.docking.org and http://blaster.docking.org
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e.g. ChemAxon, OpenEye, Schrodinger, Molinspiration, Pipeline Pilot, KNIME, many others.
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Container for discussions of software, database and methodological development.
Forum for the discussion of DOCK 3.6. Topics include: current problems, recent improvements, algorithmic ideas. http://dock.docking.org.
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Forum for the discussion of the DOCK 6 software. Topics include algorithmic weaknesses, ideas, solutions, proposals.
121 year 3 weeks ago
by John Irwin
¿What can be done if you what to use the output files of Dock3.5 in Dock6.7? I am having trouble with the file type. Dock 6.7 just accepts .mol2 files but the output files of Dock3.5 are given in .pdb ¿What can I do to transform .pdb to .mol2 files?
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This is a container for user contributed software.
Software or databases you control that you wish to share with your colleagues. We offer this container to host software that you can make available to other people in a relatively high traffic place. CAVEAT EMPTOR! We do not offer any guarantees or warranty. Use of this site and any software you find here must be entirely at your own risk.
112 years 34 weeks ago
by devl777
We are not really keen on this, but we offer this as a way to share information about compounds you might like to share with others, either via collaboration or for sale. This might be appropriate for vendors who only sell a few compounds or perhaps academic groups that might like to collaborate by making their compounds available. If you are a major vendor, you should register with ZINC and get your catalog loaded.
115 years 33 weeks ago
by Lily Chen