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Nucleic Acids Res. 2003 Jul 1;31(13):3364-6.

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

Author information

1
Dipartimento di Chimica, Università di Salerno, via Salvador Allende, I-84081 Baronissi (SA) Italy.

Abstract

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.

PMID:
12824328
PMCID:
PMC169007
[Indexed for MEDLINE]
Free PMC Article

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