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POPSCOMP: an automated interaction analysis of biomolecular complexes.

ABSTRACT: 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/.

SUBMITTER: Kleinjung J

PROVIDER: S-EPMC1160130 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature

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POPSCOMP: an automated interaction analysis of biomolecular complexes.

Kleinjung Jens J Fraternali Franca F

Nucleic acids research 20050701 Web Server issue

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 inv ...[more]

PMID: 15980485

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