ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts.

ABSTRACT: ReFOLD3 is unique in its application of gradual restraints, calculated from local model quality estimates and contact predictions, which are used to guide the refinement of theoretical 3D protein models towards the native structures. ReFOLD3 achieves improved performance by using an iterative refinement protocol to fix incorrect residue contacts and local errors, including unusual bonds and angles, which are identified in the submitted models by our leading ModFOLD8 model quality assessment method. Following refinement, the likely resulting improvements to the submitted models are recognized by ModFOLD8, which produces both global and local quality estimates. During the CASP14 prediction season (May-Aug 2020), we used the ReFOLD3 protocol to refine hundreds of 3D models, for both the refin

SUBMITTER: Adiyaman R 

PROVIDER: S-EPMC8218204 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature