Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues.

ABSTRACT: Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM. The algorithm adjusts the number of fast modes in the GNM's weighted sum calculation using the ratio of predicted and expected numbers of target residues (contact and the neighboring first-layer residues). Th

SUBMITTER: Perisic O 

PROVIDER: S-EPMC5874725 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature