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Bioinformatics Advance Access published online on December 6, 2006
Bioinformatics, 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
Received September 28, 2006
Revised November 28, 2006
Accepted December 4, 2006

Article

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

José Ignacio Garzón 1, Julio Kovacs 2, Ruben Abagyan 2, and Pablo Chacón 1 *

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


  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 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.

Associate Editor: Alex Bateman
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