Protein-Ligand Complexes


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Rapture
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Message 4832 - Posted 7 Feb 2009 1:20:20 UTC

Since the project went public September 2008, what relationships, if any, are there for the work done between proteins Trypsin, HIV Protease and P38 alpha?

How do you know how many and what type of ligands do you need for a particular protein in order to find their lowest energy state docking?

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Profile robertmiles

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Message 5539 - Posted 23 Nov 2009 10:44:57 UTC
Last modified: 23 Nov 2009 10:57:05 UTC

Here's some information on a catalog of compounds (ZINC) that might be useful in selecting what to dock to the protein under study.


http://zinc.docking.org/

http://wiki.compbio.ucsf.edu/wiki/index.php/ZINC_Database

http://en.wikipedia.org/wiki/ZINC_database

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360656/


I've seen no evidence that Docking@home is using it yet, though. I'd expect them to have to go through a list of possible ligands, and create a number of workunits for each ligand that looks suitable, give us those workunits, and then analyze the outputs to determine what the lowest energy for each of those ligands happens to be.


I notice that there's no Wiktionary page for Docking@home yet. Once it's about to get past beta test, I'd suggest creating one.

http://www.wiktionary.org/

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Message boards : Docking@Home Science : Protein-Ligand Complexes

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