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Bioinformatics Advance Access originally published online on December 6, 2006
Bioinformatics 2007 23(4):427-433; doi:10.1093/bioinformatics/btl625
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

José Ignacio Garzón , Julio Kovacs 1, Ruben Abagyan 1 and Pablo Chacón *

Centro de Investigaciones Biológicas, CSIC Ramiro de Maeztu 9, 28040 Madrid, Spain
1 Department of Molecular Biology, The Scripps Research Institute La Jolla CA 92037, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning.

Results: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage.

Availability: http://sbg.cib.csic.es/Software/ADP_EM

Contact: pablo{at}cib.csic.es

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on September 28, 2006; revised on November 28, 2006; accepted on December 4, 2006

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