PMID:12824328
| Citation |
Cavallo, L, Kleinjung, J and Fraternali, F (2003) POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res. 31:3364-6 |
|---|---|
| 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. |
| Links | |
| Keywords |
Algorithms; Amino Acids/chemistry; Hydrophobic and Hydrophilic Interactions; Internet; Macromolecular Substances; Molecular Structure; Nucleic Acids/chemistry; Proteins/chemistry; Software; Solvents/chemistry; Time Factors; User-Computer Interface |
| edit table |
Significance
You can help EcoliWiki by summarizing why this paper is useful
Useful Materials and Methods
You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.
Annotations
<protect><annotationlinks/></protect>
EcoliWiki Links
POPS_and_POPSCOMP
Category:Bioinformatics_Tools
See also
References
See Help:References for how to manage references in EcoliWiki.
