CoinFold: a web server for protein contact prediction and contact-assisted protein folding.
CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction.
Toyota Technological Institute at Chicago, Chicago, IL, USA Department of Human Genetics, University of Chicago, Chicago, IL, USA wangsheng@uchicago.edu.
Sheng
S
Wang
School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, China.
Wei
W
Li
Toyota Technological Institute at Chicago, Chicago, IL, USA.
Renyu
R
Zhang
School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Zhejiang, China.
Shiwang
S
Liu
Toyota Technological Institute at Chicago, Chicago, IL, USA jinboxu@gmail.com.
Jinbo
J
Xu
D000465:Algorithms; D000595:Amino Acid Sequence; D020169:Caspases / Q000737:chemistry* / Q000235:genetics; D003196:Computer Graphics; D020407:Internet; D000069550:Machine Learning; D008958:Models, Molecular; D011485:Protein Binding; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D055672:Static Electricity; D014584:User-Computer Interface
D020169:Caspases