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Proteins. 2018 Mar;86 Suppl 1:283-291. doi: 10.1002/prot.25387. Epub 2017 Oct 16.

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12.

Author information

1
Department of Biochemistry, University of Washington, Seattle, Washington, 98195.
2
Institute for Protein Design, University of Washington, Seattle, Washington, 98195.
3
Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195.

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.

KEYWORDS:

CASP12; Rosetta; protein interfaces; structure prediction; symmetric assemblies

PMID:
28913931
PMCID:
PMC6019630
DOI:
10.1002/prot.25387
[Indexed for MEDLINE]
Free PMC Article

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