title: POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level.
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.
authors.affiliation: Dipartimento di Chimica, Università di Salerno, via Salvador Allende, I-84081 Baronissi (SA) Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cavallo
authors.forename: Jens
authors.initials: J
authors.lastname: Kleinjung
authors.forename: Franca
authors.initials: F
authors.lastname: Fraternali
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D046911:Macromolecular Substances; D015394:Molecular Structure; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012997:Solvents / Q000737:chemistry*; D013997:Time Factors; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D046911:Macromolecular Substances; D009696:Nucleic Acids; D011506:Proteins; D012997:Solvents