POPSCOMP: an automated interaction analysis of biomolecular complexes | Zendy

Jens Kleinjung | Zendy; Franca Fraternali | Zendy

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POPSCOMP: an automated interaction analysis of biomolecular complexes

Author(s) -

Jens Kleinjung,

Franca Fraternali

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki369

Subject(s) - biology , computational biology , dna , resolution (logic) , web server , interaction network , rna , biological system , bioinformatics , computer science , biochemistry , the internet , gene , artificial intelligence , world wide web

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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