RT Journal Article
SR Electronic
T1 CONFOLD2: Improved contact-driven ab initio protein structure modeling
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 228460
DO 10.1101/228460
A1 Badri Adhikari
A1 Jianlin Cheng
YR 2017
UL http://biorxiv.org/content/early/2017/12/04/228460.abstract
AB Background Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support the contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted contacts need to be developed.Results We develop an improved contact-driven protein modeling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input. It builds models using various subsets of input contacts to explore the fold space under the guidance of a soft square energy function, and then clusters the models to obtain top five models. CONFOLD2 is benchmarked on various datasets including CASP11 and 12 datasets with publicly available predicted contacts and yields better performance than the popular CONFOLD method.Conclusion CONFOLD2 allows to quickly generate top five structural models for a protein sequence, when its secondary structures and contacts predictions at hand. CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/.