Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction.

ABSTRACT: Quantitative prediction of protein-protein binding affinity is essential for understanding protein-protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein-protein binding affinity. The potential is obtained by statistically analyzing X-ray structures of protein-protein complexes in the Protein Data Bank. This approach circumvents the complicated steps of the volume correction process and is very easy to implement in practice. It can obtain more reasonable pair potential compared with traditional PMF and shows a classic picture of nonbonded atom pair interaction as Lennard-Jones potential. To evaluate the prediction ability for protein-protein binding affinity, six test sets are examined. S

SUBMITTER: Su Y 

PROVIDER: S-EPMC2821273 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature