Distance-based reconstruction of protein quaternary structures from inter-chain contacts.

ABSTRACT: Predicting the quaternary structure of protein complex is an important problem. Inter-chain residue-residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter-chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter-chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure rando

SUBMITTER: Soltanikazemi E 

PROVIDER: S-EPMC8816881 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature