Cavallo Luigi, Kleinjung Jens, Fraternali Franca
Dipartimento di Chimica, Università di Salerno, via Salvador Allende, I-84081 Baronissi (SA) Italy.
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.
POPS（参数优化表面）是一种计算溶剂可及表面积的新方法，它基于一个可凭经验参数化的解析公式，计算速度快。已针对精确的全原子方法对原子和残基面积（后者由以氨基酸的C（α）原子和核苷酸的P原子为中心的单个球体表示）进行了优化。参数化源自不同大小和拓扑结构的蛋白质和核酸的选定数据集。基于残基的方法POPS-R已被设计为分析核糖体等大型大分子组装体的有用工具，特别适用于低分辨率结构的优化。POPS-R还允许估计复合物形成时溶剂化自由能的损失，这对于设计新的蛋白质-蛋白质和蛋白质-核酸复合物应该特别有用。程序POPS可在http://mathbio.nimr.mrc.ac.uk/~ffranca/POPS以及镜像站点http://www.cs.vu.nl/~ibivu/programs/popswww获取。
