Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

ABSTRACT: The prediction of protein-protein kinetic rate constants provides a fundamental test of our understanding of molecular recognition, and will play an important role in the modeling of complex biological systems. In this paper, a feature selection and regression algorithm is applied to mine a large set of molecular descriptors and construct simple models for association and dissociation rate constants using empirical data. Using separate test data for validation, the predicted rate constants can be combined to calculate binding affinity with accuracy matching that of state of the art empirical free energy functions. The models show that the rate of association is linearly related to the proportion of unbound proteins in the bound conformational ensemble relative to the unbound conformational

SUBMITTER: Moal IH 

PROVIDER: S-EPMC3257286 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature