Automatic structure prediction of oligomeric assemblies using Robetta in CASP12
By Hahnbeom Park, David E. Kim, Sergey Ovchinnikov, David Baker, Frank DiMaio. 2017
53 citations recorded by the source corpus.
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.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Jeffrey J. Gray
- David Baker
- Hahnbeom Park
- David E. Kim
- Gyu Rie Lee
- Qian Cong
- Shourya S. Roy Burman
- Ivan Anishchanka
In Molecular Biology
- Jeffrey J. Gray
- David Baker
- Hahnbeom Park
- David E. Kim
- Shourya S. Roy Burman
- Gyu Rie Lee
- Qian Cong
- Remy A. Yovanno
Citations in the corpus
- High-accuracy refinement using Rosetta in CASP13 (2019, methodology): “The Rosetta symmetry modeling machinery used for homo-oligomer comparative modeling 17,18 was incorporated into the refinement pipeline in this CASP.”
- Flexible backbone assembly and refinement of symmetrical homomeric complexes (2018, background): “Instead, incorporating symmetry information while homology modeling provides a promising avenue, which servers like Robetta (Park et al., 2018), SWISS-MODEL Oligo (Bertoni et al., 2017) and GalaxyHomomer (Baek et al., 2017) have recently demonstrated.”