ADL: Treatment of Cyclic Substances by AutoDock

Michel Sanner sanner at scripps.edu
Fri Oct 2 08:43:53 PDT 2020


Hello

We have developed a peptide-specific docking engine called AutoDock CrankPep (ADCP in short). It is able to dock peptides cyclized thought their backbone (i.e. head-to-tail) and with up to 2 disulfide bridges between cysteine side chains starting from the peptide’s sequence, see: https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.9b00557

You can download the software and find documentation at https://ccsb.scripps.edu/adcp/

Best regards

-Michel


From: <autodock-bounces at scripps.edu> on behalf of Edmund R Marinelli <edmundmarinelli at gmail.com>
Reply-To: "autodock at scripps.edu" <autodock at scripps.edu>
Date: Thursday, October 1, 2020 at 9:07 PM
To: "autodock at scripps.edu" <autodock at scripps.edu>
Subject: ADL: Treatment of Cyclic Substances by AutoDock

How are cyclic substances treated with respect to generation of conformers ,
by AutoDock and AutoDock Vina.  As torsional angles are limited due to the
constraints of the cyclic structure , is there an algorithm that accounts
for that?  The question is relevant to relatively small cycles but also to
cyclic peptides, of which many interesting ones are from 8-20 residues .



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