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

Luigi Cavallo·Jens Kleinjung·Franca Fraternali
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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.

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AlgorithmsAmino AcidsHydrophobic and Hydrophilic InteractionsInternetMacromolecular SubstancesMolecular StructureNucleic AcidsProteinsSoftwareSolventsTime FactorsUser-Computer InterfaceJournal Article

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Luigi Cavallo, Jens Kleinjung, Franca Fraternali. 2003-07-01. POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level.. https://doi.org/10.1093/nar%2Fgkg601

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