scholarly journals Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

2011 ◽  
Vol 79 (S10) ◽  
pp. 147-160 ◽  
Author(s):  
Dong Xu ◽  
Jian Zhang ◽  
Ambrish Roy ◽  
Yang Zhang
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Structure Refinement ◽  
Structure Modeling ◽  
Protein Structure Modeling

scholarly journals CONFOLD2: Improved contact-driven ab initio protein structure modeling

2017 ◽  
Author(s):  
Badri Adhikari ◽  
Jianlin Cheng
Keyword(s):  
Protein Structure ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Structural Models ◽  
Prediction Methods ◽  
Structure Modeling ◽  
Residue Contact ◽  
Protein Structure Modeling

AbstractBackgroundContact-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.ResultsWe 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.ConclusionCONFOLD2 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/.

scholarly journals Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments

2007 ◽  
Vol 23 (19) ◽  
pp. 2558-2565 ◽  
Author(s):  
N. Fernandez-Fuentes ◽  
B. K. Rai ◽  
C. J. Madrid-Aliste ◽  
J. Eduardo Fajardo ◽  
A. Fiser
Keyword(s):  
Protein Structure ◽  
Structure Modeling ◽  
Protein Structure Modeling ◽  
Multiple Templates

scholarly journals RosettaBackrub--a web server for flexible backbone protein structure modeling and design

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W569-W575 ◽  
Author(s):  
F. Lauck ◽  
C. A. Smith ◽  
G. F. Friedland ◽  
E. L. Humphris ◽  
T. Kortemme
Keyword(s):  
Protein Structure ◽  
Web Server ◽  
Structure Modeling ◽  
Protein Structure Modeling

scholarly journals AS2TS system for protein structure modeling and analysis

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W111-W115 ◽  
Author(s):  
A. Zemla ◽  
C. E. Zhou ◽  
T. Slezak ◽  
T. Kuczmarski ◽  
D. Rama ◽  
...  
Keyword(s):  
Protein Structure ◽  
Structure Modeling ◽  
Modeling And Analysis ◽  
Protein Structure Modeling
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