Work

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12

Year: 2017

Type: article

Abstract: Many naturally occurring protein systems function primarily as symmetric assemblies. Prediction of the quaternary structure of these assemblies is an important biological problem. This article describes automated tools we have developed for predicting the structures of symmetric protein assemblies in the Robetta structure prediction server. We assess the performance of this pipeline on a set of targets from the recent CASP12/CAPRI blind quaternary structure prediction experiment. Our approach successfully predicted 5 of 7 symmetric assemblies in this challenge, and was assessed as the best participating server group, and 1 of only 2 groups (human or server) with 2 predictions judged as high quality by the assessors. We also assess the method on a broader set of 22 natively symmetric CASP12 targets, where we show that oligomeric modeling can improve the accuracy of monomeric structure determination, particularly in highly intertwined oligomers.

Source: Proteins Structure Function and Bioinformatics

DOI: 10.1002/prot.25387

Authors: Hahnbeom Park, David E. Kim, Sergey Ovchinnikov, David Baker, Frank DiMaio

Institutions: University of Washington, Howard Hughes Medical Institute

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: National Institute of General Medical Sciences

Awards: Training in Cellular and Molecular Biology, Protein structure determination from low-resolution experimental data