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

Bioinformatics. 2007 Feb 15;23(4):427-33. doi: 10.1093/bioinformatics/btl625. Epub 2006 Dec 6.

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.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Binding Sites
  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping / methods*
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, Protein / methods*

Substances

  • Proteins