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I-TASSER QUARK LOMETS COACH COFACTOR MUSTER SEGMER FG-MD ModRefiner REMO SPRING COTH BSpred SVMSEQ ANGLOR BSP-SLIM SAXSTER ThreaDom EvoDesign GPCR-I-TASSER

TM-score TM-align MMalign NWalign EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP TM-fold DECOYS POTENTIAL RW CASP7 CASP8 CASP9 CASP10 CASP11

Publications in Yang Zhang Lab
( >> Most Cited Publications)

2014  
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang
The I-TASSER Suite: Protein structure and function prediction.
Nature Methods, in press (2014).
Ronan Keegan, Jaclyn Bibby, Jens Thomas, Dong Xu, Yang Zhang, Olga Mayans, Martyn Winn, Daniel Rigden
Exploring speed and performance of Molecular Replacement with AMPLE using QUARK ab initio protein models.
Acta Crystallographica Section D, in press (2014).
Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen
Bioimaging based detection of mislocalized proteins in human cancers by semi-supervised learning.
Bioinformatics, in press (2014).
Grant Holdren, David Rosenthal, Jianyi Yang, Amber Bates, Carol Fischer, Yang Zhang, Nicole Brogden, Kim Brogden
Antimicrobial activity of chemokine CXCL10 for dermal and oral microorganisms.
Antibiotics, in press (2014).
Hongying Du, Jeffrey R Brender, Jian Zhang, Yang Zhang
Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.
Methods, in press (2014).
[PDF]
Shu Quan, Lili Wang, Evgeniy V Petrotchenko, Karl AT Makepeace, Scott Horowitz, Jianyi Yang, Yang Zhang, Christoph H Borchers, James CA Bardwell
Super Spy variants implicate flexibility in chaperone action.
eLife, 3: e01584 (2014).
[PDF]
Derek S Borgwardt, Aaron D. Martin, Jonathan R Van Hemert, Jianyi Yang, Carol L Fischer, Erica N Recker, Prashant R Nair, Robinson Vidva, Shwetha Chandrashekaraiah, Ann Progulske-Fox, David Drake, Joseph E Cavanaugh, Shireen Vali, Yang Zhang, Kim A Brogden
Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses.
Scientific Reports, 4: 3904 (2014).
[PDF]
Yang Zhang
Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.
Proteins: Structure, Function, and Bioinformatics, 82: 175-187 (2014).
[PDF] [Support Information]
Andras Szilagyi, Yang Zhang
Template-based structure modeling of protein-protein interactions.
Current Opinion in Structural Biology, 24: 10-23 (2014).
[PDF]
2013  
Pralay Mitra, David Shultis, Jeffrey R Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang
An evolution-based approach to de novo protein design and case study on Mycobacterium Tuberculosis.
PLoS Computational Biology, 9: e1003298 (2013).
[PDF] [Support Information]
Renxiang Yan, Dong Xu, Jianyi Yang, Sara Walker, Yang Zhang
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction.
Scientific Reports, 3: 2619 (2013).
[PDF] [Support Information]
Jianyi Yang, Ambrish Roy, Yang Zhang
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment.
Bioinformatics, 29: 2588 (2013).
[PDF] [Support Information] [Server]
Dong Xu, Hua Li, Yang Zhang
Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition.
Journal of Computational Biology, 20: 805-816 (2013).
Pralay Mitra, David Shultis, Yang Zhang
EvoDesign: de novo protein design based on structural and evolutionary profiles.
Nucleic Acids Research, 41: W273-W280 (2013).
[PDF] [Support Information] [Server] [This paper was highlighted by Faculty of 1000]
Zhiding Xue, Dong Xu, Yan Wang, Yang Zhang
ThreaDom: Extracting Protein Domain Boundary Information from Multiple Threading Alignments.
Bioinformatics, 29: i247-i256 (2013).
[PDF] [Server]
Jiaqi Fu, Song Ling, Ying Liu, Jianyi Yang, Shirly Naveh, Margaret Hannah, Chaim Gilon, Yang Zhang, Joseph Holoshitz
A Small Shared Epitope-Mimetic Compound Potently Accelerates Osteoclast-Mediated Bone Damage in Autoimmune Arthritis.
The Journal of Immunology, 191: 2096-2103 (2013).
[PDF]
Dong Xu, Yang Zhang
Ab Initio Structure Prediction for Escherichia coli: Towards Genome-wide Protein Structure Modeling and Fold Assignment.
Scientific Reports, 3: 1895 (2013).
[PDF] [Support Information] [Database]
Jing Yang, Richard Jang, Yang Zhang, Hongbin Shen
High-accuracy prediction of transmembrane inter-helix con-tacts and application to GPCR 3D structure modeling.
Bioinformatics, 29: 2579 (2013).
[PDF] [Support Information]
Yingying Xu, Fan Yang, Yang Zhang, Hongbin Shen
An image-based multi-label human protein subcellular localiza-tion predictor (iLocator) reveals protein mislocalizations in cancer tissues.
Bioinformatics, 29: 2032-2040 (2013).
[PDF] [Support Information]
Gyorgy Abrusan, Yang Zhang, Andras Szilagyi
Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins.
Journal of Biological Chemistry, 288: 16127-16138 (2013).
[PDF] [Support Information]
Gilbert S. Omenn, Rajasree Menon, Yang Zhang
Innovations in Proteomic Profiling of Cancers: Alternative Splice Variants as a New Class of Cancer Biomarker Candidates and Bridging of Proteomics with Structural Biology.
Journal of Proteomics, 90: 28-37 (2013).
[PDF]
Aysam Guerler, Brandon Govindarajoo, Yang Zhang
Mapping Monomeric Threading to Protein-Protein Structure Prediction.
Journal of Chemical Information and Modeling, 53: 717-725 (2013).
[PDF] [Server]
Yang Zhang, Jeffrey Skolnick
Segment assembly, structure alignment and iterative simulation in protein structure prediction.
BMC Biology, 11: 44 (2013).
[PDF]
Yongxian Fan, Yang Zhang, Hongbin Shen
LabCaS: Labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields.
Proteins: Structure, Function, and Bioinformatics, 81: 622-634 (2013).
[PDF] [Server]
Dong Xu, Hua Li, Yang Zhang
Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform.
Lecture Notes in Bioinformatics (RECOMB 2013), 7821: 304-316 (2013).
[PDF] [Server]
Gyorgy Abrusan, Andras Szilagyi, Yang Zhang, Balazs Papp
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks.
Nucleic Acids Research, 41: 3190-3200 (2013).
[PDF] [Support Information]
Dong Xu, Yang Zhang
Toward optimal fragment generations for ab initio protein structure assembly.
Proteins: Structure, Function, and Bioinformatics, 81: 229-239 (2013).
[PDF] [Support Information]
Jianyi Yang, Ambrish Roy, Yang Zhang
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.
Nucleic Acids Research, 41: D1096-1103 (2013).
[PDF] [Database]
2012  
Ambrish Roy, Yang Zhang
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement.
Structure, 20: 987-997 (2012).
[PDF] [Support Information] [This paper was highlighted by Faculty of 1000]
Yang Yang, Sulayman Dib-Hajj, Jian Zhang, Yang Zhang, Lynda Tyrrell, Mark Estacion
Structural modelling and mutant cycle analysis predict pharmacoresponsiveness of a Nav1.7 mutant channel.
Nature Communications, 3: 1186 (2012).
[PDF] [Support Information]
Owen W. Nadeau, Laura A. Lane, Dong Xu, Jessica Sage, Timothy S. Priddy, Antonio Artigues, Maria T. Villar, Qing Yang, Carol V. Robinson, Yang Zhang and Gerald M. Carlson
Structure and Location of the Regulatory beta Subunits in the ([alpha][beta][gamma][delta])4 Phosphorylase Kinase Complex.
Journal of Biological Chemistry, 287: 36651-36661 (2012).
[PDF] [Commentary] [This paper was selected as the Best Paper of 2012 in JBC]
Haiyou Deng, Ya Jia, Yanyu Wei, Yang Zhang
What is the best reference state for designing statistical atomic potentials in protein structure prediction?
Proteins: Structure, Function, and Bioinformatics, 80: 2311-2322 (2012).
[PDF] [Support Information]
Ambrish Roy, Jianyi Yang, Yang Zhang
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation.
Nucleic Acids Research, 40: W471-W477 (2012).
[PDF] [Support Information] [Server]
Ambrish Roy, Yang Zhang
Protein structure prediction.
Encyclopedia of Life Sciences, DOI: 10.1002/9780470015902.a0003031.pub2 (2012).
[PDF]
Leonardo Garma, Srayanta Mukherjee, Pralay Mitra, Yang Zhang
How many protein-protein interactions types exist in nature?
PLoS One, 7: e38913 (2012).
[PDF] [Support Information]
Dong Xu, Yang Zhang
Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field.
Proteins: Structure, Function, and Bioinformatics, 80: 1715-1735 (2012).
[PDF] [Support Information] [Server] [This paper was ranked the Most Cited Articles in 2012 Proteins]
Liu Hong, Xianghong Qi, Yang Zhang
Dissecting the Kinetic Process of Amyloid Fiber Formation through Asymptotic Analysis.
Journal of Physical Chemistry, B 116: 6611-6617 (2012).
[PDF] [Support Information] [Server]
Xianghong Qi, Liu Hong, Yang Zhang
A Variational Model for Oligomer-Formation Process of GNNQQNY Peptide from Yeast Prion Protein Sup35.
Biophysical Journal, 102: 597-605 (2012).
[PDF] [Support Information] [Server]
Andras Szilagyi, Yang Zhang
Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures.
Journal of Molecular Biology, 415: 221-235 (2012).
[PDF] [Support Information]
Iris Dror, Shula Shazman, Srayanta Mukherjee, Yang Zhang, Fabian Glaser, Yael Mandel-Gutfreund
Predicting nucleic acid binding interfaces from structural models of proteins.
Proteins: Structure, Function, and Bioinformatics, 80: 482-489 (2012).
[PDF]
Yunqi Li, Jian Zhang, David Tai, C. Russell Middaugh, Yang Zhang, Jianwen Fang
PROTS: A fragment based protein thermo-stability potential.
Proteins: Structure, Function, and Bioinformatics, 80: 81-92 (2012).
[PDF]
Huisun Lee, Yang Zhang
BSP-SLIM: A blind low-resolution ligand-protein docking approach using predicted protein structures.
Proteins: Structure, Function, and Bioinformatics, 80: 93-110 (2012).
[PDF] [Server]
2011  
Jian Zhang, Yu Liang, Yang Zhang
Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling.
Structure, 19: 1784-1795 (2011).
[PDF] [Support Information] [Commentary] [Server] [This paper is highlighted in Structure 2011 and PSI|Nature]
Dong Xu, Yang Zhang
Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization.
Biophysical Journal, 101: 2525-2534 (2011).
[PDF] [Support Information] [Server]
Rajasree Menon, Ambrish Roy, Srayanta Mukerjee, Saveliy Belkin, Yang Zhang, Gilbert Omenn
Functional Implications of Structural Predictions for Alternative Splice Proteins Expressed in Her2/neu-induced Breast Cancers.
Journal of Proteome Research, 10: 5503-5511 (2011).
[PDF] [Support Information]
Marcelo Augusto dos Reis, Ricardo Aparicio, Yang Zhang
Improving protein template recognition by using small angle X-ray scattering profiles.
Biophysical Journal, 101: 2770-2781 (2011).
[PDF] [Support Information] [Server]
Kyle E. Kemege, John M. Hickey, Scott Lovell, Kevin P. Battaile, Yang Zhang, P. Scott Hefty
Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes.
Journal of Bacteriology, 193: 6517-6528 (2011).
[PDF]
Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang
A Protocol for Computer-Based Protein Structure and Function Prediction.
Journal of Visualized Experiments, 57: e3259 (2011).
[PDF] [Server] [Vedio]
Sitao Wu, Andras Szilagyi, Yang Zhang
Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions.
Structure, 19: 1182-1191 (2011).
[PDF] [Support Information]
Dong Xu, Jian Zhang, Ambrish Roy, Yang Zhang
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.
Proteins: Structure, Function, and Bioinformatics, 79 (Suppl 10): 147-160 (2011).
[PDF]
Hongying Du, Zhide Hu, Andrea Bazzoli, Yang Zhang
Prediction of inhibitory activity of epidermal growth factor receptor inhibitors using grid search-projection pursuit regression method.
PLoS One, 6: e22367 (2011).
[PDF] [Support Information]
Carolyn A. Rankin, Ambrish Roy, Yang Zhang, Mark Richter
Parkin, A Top Level Manager in the Cell's Sanitation Department.
The Open Biochemistry Journal, 5: 9-26 (2011).
[PDF]
Srayanta Mukherjee, Yang Zhang
Protein-protein complex structure predictions by multimeric threading and template recombination.
Structure, 19: 955-966 (2011).
[PDF] [Support Information] [Server]
Liu Hong, Xianghong Qi, Yang Zhang
A lattice-gas model for amyloid fibril aggregation.
Europhysics Letters, 94: 68006 (2011).
[PDF]
Andrea Bazzoli, Andrea G. B. Tettamanzi, Yang Zhang
Computational Protein Design and Large-Scale Assessment by I-TASSER Structure Assembly Simulations.
Journal of Molecular Biology, 407: 764-776 (2011).
[PDF] [Support Information]
2010  
Jian Zhang, Yang Zhang
GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation.
Bioinformatics, 26: 3004-3005 (2010).
[PDF] [Support Information] [Server]
Jian Zhang, Yang Zhang
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction.
PLoS One, 5: e15386 (2010).
[PDF] [Server]
Sitao Wu, Yang Zhang
Recognizing Protein Substructure Similarity Using Segmental Threading.
Structure, 18: 858-867 (2010).
[PDF] [Support Information] [Server]
Ambrish Roy, Alper Kucukural, Yang Zhang
I-TASSER: a unified platform for automated protein structure and function prediction.
Nature Protocols, 5: 725-738 (2010).
[PDF] [Server]
Jason A. Somarelli, Annia Mesa, Ambrish Roy, Yang Zhang, Rene J. Herrera
A three-dimensional model of the U1 small nuclear ribonucleoprotein particle.
Entomological Research, 40: 104-112 (2010).
[PDF]
Srayanta Mukherjee, Andras Szilagyi, Ambrish Roy, Yang Zhang
Genome-wide protein structure prediction.
Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, Chapter 11, Edited by Andrzej Kolinski, (Springer-London, 2010), P. 255-280.
[PDF]
Ambrish Roy, Sitao Wu, Yang Zhang
Composite approaches to protein tertiary structure prediction: A case-study by I-TASSER.
Protein Structure Prediction: Method and Algorithms, Chapter 11, Edited by H. Rangwala and G. Karypis, (Wiley, 2010), P. 243-263.
[PDF]
Jinrui Xu, Yang Zhang
How significant is a protein structure similarity with TM-score= 0.5?
Bioinformatics, 26: 889-895 (2010).
[PDF] [Support Information] [Server]
2009  
Yang Zhang
Protein structure prediction: when is it useful?
Current Opinion in Structural Biology, 19: 145-155 (2009).
[PDF] [This paper was ranked the Most Cited Current Opinion in Structural Biology Articles]
Srayanta Mukherjee, Yang Zhang
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Research, 37: e83 (2009).
[PDF] [Support Information] [Server]
Dong Xu, Yang Zhang
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.
PLoS One, 4: e8140 (2009).
[PDF] [Server]
Jooyoung Lee, Sitao Wu, Yang Zhang
Ab initio protein structure prediction.
From Protein Structure to Function with Bioinformatics, Chapter 1, Edited by D. J. Rigden, (Springer-London, 2009), P. 1-26.
[PDF]
Yunqi Li, Yang Zhang
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.
Proteins: Structure, Function, and Bioinformatics, 76: 665-676 (2009).
[PDF] [Server]
Yang Zhang
I-TASSER: Fully automated protein structure prediction in CASP8.
Proteins: Structure, Function, and Bioinformatics, 77 (Suppl 9): 100-113 (2009).
[PDF] [Support Information]
Yunqi Li, Ambrish Roy, Yang Zhang
HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.
PLoS One, 4: e6701 (2009).
[PDF] [Server]
Sitao Wu, Yang Zhang
Protein structure prediction.
Bioinformatics: Tools and Applications, Chapter 11, Edited by D. Edwards, D. Hansen and J. Stajich, (Springer-London, 2009), P. 225-242.
[PDF]
Emanuele Bultrini, Kevin Brick, Srayanta Mukherjee, Yang Zhang, Francesco Silvestrini, Pietro Alano, Elisabetta Pizzi
Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction.
BMC Genomics, 10: 445 (2009).
[PDF]
Alper Kucukural, Andras Szilagyi, Ugur Sezerman, Yang Zhang
Protein Homology Analysis for Function Prediction with Parallel Sub-Graph lsomorphism.
Chemoinformatics: Advances in Chemoinformatics and Computational Methods, Edited by H. Lodhi and Y. Yamanishi, (IGI global, 2009), P. 129-144.
[PDF]
2008  
Yang Zhang
Progress and challenges in protein structure prediction.
Current Opinion in Structural Biology, 18: 342-348 (2008).
[PDF] [This paper was ranked the Most Cited Current Opinion in Structural Biology Articles]
Sitao Wu, Yang Zhang
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction.
Bioinformatics, 24: 924-931 (2008).
[PDF] [Support Information]
Sitao Wu, Yang Zhang
ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction.
PLoS One, 3: e3400 (2008).
[PDF] [Server]
Sitao Wu, Yang Zhang
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information.
Proteins: Structure, Function, and Bioinformatics, 72: 547-556 (2008).
[PDF] [Server]
Yang Zhang
I-TASSER server for protein 3D structure prediction.
BMC Bioinformatics, 9: 40 (2008).
[PDF] [Server]
2007  
Stephan Lorenzen, Yang Zhang
Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization.
Protein Science, 16: 2716-2725 (2007).
[PDF]
Yang Zhang
Template-based modeling and free modeling by I-TASSER in CASP7.
Proteins: Structure, Function, and Bioinformatics, 69 (Suppl 8): 108-117 (2007).
[PDF]
Jeffrey Skolnick, Yang Zhang
Protein Structure Prediction.
Systems Biology, Volume I: Genomics, Edited by I. Rigoutsos and G. Stephanopoulos, (Oxford University Press, 2007), P. 187-218.
[PDF]
Sitao Wu, Yang Zhang
LOMETS: A local meta-threading-server for protein structure prediction.
Nucleic Acids Research, 35: 3375-3382 (2007).
[PDF] [Support Information] [Server]
Sitao Wu, Jeffrey Skolnick, Yang Zhang
Ab initio modeling of small proteins by iterative TASSER simulations.
BMC Biology, 5: 17 (2007).
[PDF]
Stephan Lorenzen, Yang Zhang
Identification of near-native structures by clustering protein docking conformations.
Proteins: Structure, Function, and Bioinformatics, 68: 187-194 (2007).
[PDF]
2006  
Yang Zhang, Isaac A. Hubner, Adrian K. Arakaki, Eugene Shakhnovich, Jeffrey Skolnick
On the origin and highly likely completeness of single-domain protein structures.
Proceedings of the National Academy of Sciences of USA, 103: 2605-2610 (2006).
[PDF] [Support Information]
Yang Zhang, Mark E. DeVries, Jeffrey Skolnick
Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
PLoS Computational Biology, 2: e13 (2006).
[PDF]
Vera Grimm, Yang Zhang, Jeffrey Skolnick
Benchmarking of dimeric threading and structure refinement.
Proteins: Structure, Function, and Bioinformatics, 63: 457-465 (2006).
[PDF]
Seung Yup Lee, Yang Zhang, Jeffrey Skolnick
TASSER-based refinement of NMR structures.
Proteins: Structure, Function, and Bioinformatics, 63: 451-456 (2006).
[PDF]
Haijun Zhou, Yang Zhang, Zhong-can Ou-Yang
Theoretical and computational treatments of DNA and RNA molecules.
Handbook of Theoretical and Computational Nanotechnology, Edited by M. Rieth and W. Schommers, (American Scientific Publishers, 2006), P. 419-487.
[PDF]
Shashi Bhushan Pandit, Yang Zhang, Jeffrey Skolnick
TASSER-Lite: An Automated Tool for Protein Comparative Modeling.
Biophysical Journal, 91: 4180-4190 (2006).
[PDF]
Jeffrey Skolnick, Yang Zhang, Andrzej Kolinski
Ab Initio Modelling.
Structural Genomics and High Throughput Structural Biology, Chapter 8, Edited by M. Sundstrom, M. Norin, and A. Edwards, (Taylor and Francis, 2006), P. 137-162.
2005  
Yang Zhang, Jeffrey Skolnick
TM-align: a protein structure alignment algorithm based on the TM-score.
Nucleic Acids Research, 33: 2302 (2005).
[PDF] [Server]
Yang Zhang, Jeffrey Skolnick
The protein structure prediction problem could be solved using the current PDB library.
Proceedings of the National Academy of Sciences of USA, 102: 1029 (2005).
[PDF] [This paper was highlighted in Nature Methods]
Haijun Zhou, Yang Zhang
Hierarchical Chain Model of Spider Capture Silk Elasticity.
Physical Review Letters, 94: 028104 (2005).
[PDF]
Yang Zhang, Adrian K. Arakaki, Jeffrey Skolnick
TASSER: An automated method for the prediction of protein tertiary structures in CASP6.
Proteins: Structure, Function, and Bioinformatics, 61 (Suppl 7): 91-98 (2005).
[PDF]
2004  
Yang Zhang, Jeffrey Skolnick
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.
Biophysical Journal, 87: 2647 (2004).
[PDF]
Wei Li, Yang Zhang, Jeffrey Skolnick
Application Of Sparse NMR Restraints To Large-Scale Protein Structure Prediction.
Biophysical Journal, 87: 1241 (2004).
[PDF]
Yang Zhang, Jeffrey Skolnick
Scoring Function for Automated Assessment of Protein Structure Template Quality.
Proteins: Structure, Function, and Bioinformatics, 57: 702 (2004).
[PDF] [Correction] [Server]
Yang Zhang, Jeffery Skolnick
SPICKER: A clustering approach to identify near-native protein folds.
Journal of Computational Chemistry, 25: 865 (2004).
[PDF]
Yang Zhang, Jeffrey Skolnick
Automated structure prediction of weakly homologous proteins on a genomic scale.
Proceedings of the National Academy of Sciences of USA, 101: 7594 (2004).
[PDF]
Jeffrey Skolnick, Daisuke Kihara, Yang Zhang
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm.
Proteins: Structure, Function, and Bioinformatics, 56: 502 (2004).
[PDF]
Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
Bioinformatics, 20: 511 (2004).
[PDF]
2003  
Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng Janet Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, Jeffrey Skolnick
TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data.
Proteins: Structure, Function, and Bioinformatics, 53: 290 (2003).
[PDF]
Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick
Touchstone II: A new approach to ab initio protein Structure Prediction.
Biophysical Journal, 85: 1145 (2003).
[PDF]
Jeffrey Skolnick, Yang Zhang, Adrian K. Arakaki, Andrzej Kolinski, Michal Boniecki, Andras Szilaqyi, Daisuke Kihara
Touchstone: A Unified Approach to Protein Structure Prediction.
Proteins: Structure, Function, and Bioinformatics, S53: 469-479 (2003).
[PDF]
2002  
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Elastic theories of single DNA molecules.
Physica, A306: 359 (2002).
[PDF]
Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski, Jeffrey Skolnick
Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma Genitalium Genome.
Proceedings of the National Academy of Sciences of USA, 99: 5993 (2002).
[PDF]
M. Dessinges, B. Maier, Yang Zhang, M. Peliti, D. Bensimon, V. Croquette
Stretching single stranded DNA, a model polyelectrolyte.
Physical Review Letters, 89: 248102 (2002).
[PDF]
Yang Zhang, Daisuke Kihara, Jeffrey Skolnick
Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding.
Proteins: Structure, Function, and Bioinformatics, 48: 192 (2002).
[PDF]
2001  
Yang Zhang, Haijun Zhou, Zhongcan Ouyang
Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions.
Biophysical Journal, 81: 1133 (2001).
[PDF]
Haijun Zhou, Yang Zhang
Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?
Journal of Chemical Physics, 114: 8694 (2001).
[PDF]
Haijun Zhou, Yang Zhang, Zhongcan Ouyang, Xi Z. Feng, Stuart M. Lindsay, Pichumani Balagurumoorthy, Rodney E. Harrington
Conformation and Rigidity of DNA Microcircles Containing waf1 Response Element for p53 Regulatory Protein.
Journal of Molecular Biology, 306: 227 (2001).
[PDF]
Yang Zhang, Jeffrey Skolnick
Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures.
Journal of Chemical Physics, 115: 5027 (2001).
[PDF]
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Stretch-induced hairpin-coil transitions in designed polynucleotide chains.
Physical Review Letters, 86: 356 (2001).
[PDF]
2000  
Yang Zhang, Haijun Zhou, Zhongcan Ouyang
Monte Carlo implementation of supercoiled double-stranded DNA.
Biophysical Journal, 78: 1979 (2000).
[PDF]
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments.
Physical Review, E62: 1045 (2000).
[PDF]
Yang Zhang
Approach to Monte Carlo calculation of the buckling of supercoiled DNA loops.
Physical Review, E62, RAPID COMMUNICATIONS: 5923 (2000).
[PDF]
Csaba Boros, Tachung Meng, Richard Rittel, Karsten Tabelow, Yang Zhang
Formation of color-singlet gluon clusters and inelastic diffractive scattering.
Physical Review, D61: 094010 (2000).
[PDF]
1999  
Tachung Meng, Richard Rittel, Yang Zhang
Inelastic Diffraction and Color-Singlet Gluon Clusters in High-Energy Hadron-Hadron and Lepton-Hadron Collisions.
Physical Review Letters, 82: 2044 (1999).
[PDF]
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Bending and Base-Stacking Interactions in Double-Stranded DNA.
Physical Review Letters, 82: 4560 (1999).
[PDF]

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