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PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004) Scoring Function for Automated Assessment of Protein Structure Template Quality
J. McCammon, B. Gelin, M. Karplus (1977)
Dynamics of folded proteinsNature, 267
P. Bradley, L. Malmström, Bin Qian, Jack Schonbrun, D. Chivian, David Kim, J. Meiler, K. Misura, D. Baker (2005)
Free modeling with Rosetta in CASP6Proteins: Structure, 61
Roy (2010)
I-TASSER: a unified platform for automated protein structure and function predictionNat Protoc, 5
Yang Zhang, J. Skolnick (2005)
TM-align: a protein structure alignment algorithm based on the TM-scoreNucleic Acids Research, 33
Dong Xu, Jian Zhang, Ambrish Roy, Yang Zhang (2011)
Automated protein structure modeling in CASP9 by I‐TASSER pipeline combined with QUARK‐based ab initio folding and FG‐MD‐based structure refinementProteins: Structure, 79
Sitao Wu, A. Szilágyi, Yang Zhang (2011)
Improving protein structure prediction using multiple sequence-based contact predictions.Structure, 19 8
Zhang (2008)
I-TASSER server for protein 3D structure predictionBMC Bioinformatics, 9
Alan Stevens (2022)
Monte-Carlo Simulation
Jian Zhang, Yang Zhang (2010)
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure PredictionPLoS ONE, 5
Sitao Wu, Yang Zhang (2007)
LOMETS: A local meta-threading-server for protein structure predictionNucleic Acids Research, 35
D. Eisenberg, R. Lüthy, J. Bowie (1997)
VERIFY3D: assessment of protein models with three-dimensional profiles.Methods in enzymology, 277
Jinrui Xu, Yang Zhang (2010)
How significant is a protein structure similarity with TM-score = 0.5?Bioinformatics, 26 7
Yang Zhang, J. Skolnick (2004)
SPICKER: A clustering approach to identify near‐native protein foldsJournal of Computational Chemistry, 25
Yang Zhang, J. Skolnick (2005)
The protein structure prediction problem could be solved using the current PDB library.Proceedings of the National Academy of Sciences of the United States of America, 102 4
Yang Zhang (2007)
Template‐based modeling and free modeling by I‐TASSER in CASP7Proteins: Structure, 69
Yang Zhang, J. Skolnick (2004)
Automated structure prediction of weakly homologous proteins on a genomic scale.Proceedings of the National Academy of Sciences of the United States of America, 101 20
Hongyi Zhou, Yaoqi Zhou (2002)
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability predictionProtein Science, 11
M. Levitt, A. Warshel (1975)
Computer simulation of protein foldingNature, 253
Protocol Introduction
BK Lee (2012)
10th Community wide experiment on the critical assessment of techniques for protein structure prediction
A. Liwo, Jooyoung Lee, D. Ripoll, J. Pillardy, H. Scheraga (1999)
Protein structure prediction by global optimization of a potential energy function.Proceedings of the National Academy of Sciences of the United States of America, 96 10
(2012)
Domain definition and classification. In: 10th Community wide experiment on the critical assessment of techniques for protein structure prediction
Zina Zhang, C. Chuong, Maksim Plikus, Zinazhang, Cheng-Mingchuong, Angeles
Pubfocus: Semantic Medline/pubmed Citations Analytics through Integration of Controlled Biomedical Dictionaries and Ranking Algorithm Pubfocus:semanticmedline/pubmedcitations Analyticsthroughintegrationofcontrolledbiomedical Dictionariesandrankingalgorithm
S. Altschul, Thomas Madden, A. Schäffer, Jinghui Zhang, Zheng Zhang, W. Miller, D. Lipman (1997)
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Nucleic acids research, 25 17
Sitao Wu, Yang Zhang (2008)
A comprehensive assessment of sequence-based and template-based methods for protein contact predictionBioinformatics, 24 7
Sitao Wu, Yang Zhang (2008)
MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure informationProteins: Structure, 72
K. Simons, C. Kooperberg, E. Huang, D. Baker (1997)
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.Journal of molecular biology, 268 1
A. Sali, T. Blundell (1993)
Comparative protein modelling by satisfaction of spatial restraints.Journal of molecular biology, 234 3
Jian Zhang, Yu Liang, Yang Zhang (2011)
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling.Structure, 19 12
J. Klepeis, Yinan Wei, M. Hecht, C. Floudas (2004)
Ab initio prediction of the three‐dimensional structure of a de novo designed protein: A double‐blind case studyProteins: Structure, 58
Zhidong Xue, Dong Xu, Yan Wang, Yang Zhang (2013)
ThreaDom: extracting protein domain boundary information from multiple threading alignmentsBioinformatics, 29
Dong Xu, Yang Zhang (2013)
Toward optimal fragment generations for ab initio protein structure assemblyProteins: Structure, 81
Wu (2007)
Ab initio modeling of small proteins by iterative TASSER simulationsBMC Biol, 5
Dong Xu, Yang Zhang (2012)
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force fieldProteins: Structure, 80
Min-Yi Shen, A. Sali (2006)
Statistical potential for assessment and prediction of protein structuresProtein Science, 15
Sitao Wu, Yang Zhang (2010)
Recognizing protein substructure similarity using segmental threading.Structure, 18 7
Yang Zhang, A. Kolinski, J. Skolnick (2003)
TOUCHSTONE II: a new approach to ab initio protein structure prediction.Biophysical journal, 85 2
Composite Protein Structure Prediction in CASP10 PROTEINS 13
P. Lewis, F. Momany, H. Scheraga (1971)
Folding of polypeptide chains in proteins: a proposed mechanism for folding.Proceedings of the National Academy of Sciences of the United States of America, 68 9
Zhang (2004)
Scoring function for automated assessment of protein structure template qualityProteins, 57
Yunqi Li, Yang Zhang (2009)
REMO: A new protocol to refine full atomic protein models from C‐alpha traces by optimizing hydrogen‐bonding networksProteins: Structure, 76
Yang Zhang (2009)
I‐TASSER: Fully automated protein structure prediction in CASP8Proteins: Structure, 77
We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I‐TASSER and QUARK for both free‐modeling (FM) and template‐based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK‐based ab initio models as probes allows the detection of distant‐homology templates which might be ignored by the traditional sequence profile‐based threading alignment algorithms. Further template assembly refinement by I‐TASSER resulted in successful folding of two medium‐sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I‐TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading‐constrained ab initio folding models can consistently improve the quality of the full‐length models as assessed by the GDT‐HA and hydrogen‐bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium‐size proteins (especially beta‐proteins) for nonhomologous targets. Further developments of sensitive fold‐recognition and ab initio folding methods are critical for solving these problems. Proteins 2014; 82(Suppl 2):175–187. © 2013 Wiley Periodicals, Inc.
Proteins: Structure Function and Bioinformatics – Wiley
Published: Feb 1, 2014
Keywords: ; ; ; ; ;
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