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

Nucleic Acids Res. 2003 Jul 1;31(13):3364-6. doi: 10.1093/nar/gkg601.


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.

MeSH terms

  • 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


  • Amino Acids
  • Macromolecular Substances
  • Nucleic Acids
  • Proteins
  • Solvents