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Nucleic Acids Research, 2003, Vol. 31, No. 13 3364-3366
© 2003 Oxford University Press

POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level

Luigi Cavallo, Jens Kleinjung1 and Franca Fraternali*,2

Dipartimento di Chimica, Università di Salerno, via Salvador Allende, I-84081 Baronissi (SA) Italy 1 Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, De Boelelaan, 1081A, 1081 HV Amsterdam, The Netherlands 2 Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK

*To whom correspondence should be addressed. Tel: +44 2088162250; Fax: +44 2089138545; Email: ffranca{at}nimr.mrc.ac.uk

POPS (Parameter OPtimsed Surfaces) is a new method to calculate solvent accessible surface areas, which is based on an empirically parameterisable analytical formula and fast to compute. Atomic and residue areas (the latter represented by a single sphere centered on the C{alpha} atom of amino acids and at the P atom of nucleotides) have been optimised versus accurate all-atom methods. The parameterisation has been derived from a selected dataset of proteins and nucleic acids of different sizes and topologies. The residue based approach POPS-R, has been devised as a useful tool for the analysis of large macromolecular assemblies like the ribosome and it is specially suited for the refinement of low resolution structures. POPS-R also allows for estimates of the loss of free energy of solvation upon complex formation, which should be particularly useful for the design of new protein–protein and protein–nucleic acid complexes. The program POPS is available at http://mathbio.nimr.mrc.ac.uk/~ffranca/POPS and at the mirror site http://www.cs.vu.nl/~ibivu/programs/popswww.


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