Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.

ABSTRACT: Fast Fourier transform (FFT) correlation methods of protein-protein docking, combined with the clustering of low energy conformations, can find a number of local minima on the energy surface. For most complexes, the locations of the near-native structures can be constrained to the 30 largest clusters, each surrounding a local minimum. However, no reliable further discrimination can be obtained by energy measures because the differences in the energy levels between the minima are comparable with the errors in the energy evaluation. In fact, no current scoring function accounts for the entropic contributions that relate to the width rather than the depth of the minima. Since structures at narrow minima loose more entropy, some of the nonnative states can be detected by determining whether or

SUBMITTER: Kozakov D 

PROVIDER: S-EPMC2823634 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature