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Nucleic Acids Research 2005 33(Web Server Issue):W342-W346; doi:10.1093/nar/gki369
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Article

POPSCOMP: an automated interaction analysis of biomolecular complexes

Jens Kleinjung and Franca Fraternali1,*

Bioinformatics Unit, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081A, 1081HV Amsterdam, The Netherlands 1Division of Mathematical Biology, National Institute for Medical Research Mill Hill, London NW7 1AA, UK

*To whom correspondence should be addressed. Tel: +44 20 8816 2250; Fax: +44 20 8913 8545; Email: ffranca{at}nimr.mrc.ac.uk

Received February 14, 2005. Revised March 3, 2005. Accepted March 3, 2005.

Large-scale analysis of biomolecular complexes reveals the functional network within the cell. Computational methods are required to extract the essential information from the available data. The POPSCOMP server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, DNA or RNA molecules. The server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are involved in complex formation, to pinpoint conformational changes and to estimate molecular interaction energies. The analysis can be performed on a per-atom level or alternatively on a per-residue level for low-resolution structures. Here, we present an analysis of ribosomal structures in complex with various antibiotics to exemplify the potential and limitations of automated complex analysis. The POPSCOMP server is accessible at http://ibivu.cs.vu.nl/programs/popscompwww/.


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