MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.

ABSTRACT: Molecular replacement (MR) has commonly been employed to derive the phase information in protein crystal X-ray diffraction, but its success rate decreases rapidly when the search model is dissimilar to the target. MR-REX has been developed to perform an MR search by replica-exchange Monte Carlo simulations, which enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization. MR-REX was tested on a set of 1303 protein structures of different accuracies and successfully placed 699 structures at positions that have an r.m.s.d. of below 2 Å to the target position, which is 10% higher than was obtained by Phaser. However, cases studies show that many of the models for which Phaser failed and MR-REX succeeded can be solved by Phaser by pruning them and u

SUBMITTER: Virtanen JJ 

PROVIDER: S-EPMC6038387 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature