[Dock-fans] dock3.5.54

[John J. Irwin]

Hi Barbara

Here are the references that explain how DOCK 3.5.54 works:

Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple
ligand conformations. /Curr Top Med Chem/* 5* (8), 739-49 (2005).
[Pubmed
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16101414&query_hl=1&itool=pubmed_docsum> | Download
PDF <http://shoichetlab.compbio.ucsf.edu/publications/lorber_reprint.pdf>]

Lorber DM, Shoichet BK. Flexible ligand docking using conformational
ensembles. /Protein Science/* 7*, 938-950 (1998). [Pubmed
<http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9568900&dopt=Abstract> | DOI
<http://dx.doi.org/10.1021/jm980343w>]

as cited on the web page 
http://shoichetlab.compbio.ucsf.edu/publications.php

In short, we do not use anchor-and-grow as in DOCK 4, but we enumerate
conformations in advance and dock them all at once, as an ensemble, and
then prune the tree to find the best pose.  This is the only way we have
found to be able to sample 10^6 implied conformations in under one cpu
second.

Good docking!

John
UCSF DOCK Team


Collignon, Barbara C. wrote:
> Hi everybody,
>
>
> I use dock6.2. 
>
> Is the anchor-and-grow algorithm implemented in dock3.5.54 ?
>
> Barbara 
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>   
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