Publications in Yang Zhang Lab

(Most Cited Articles Published Recently)

2012
	Jianyi Yang, Ambrish Roy, Yang Zhang BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Research, in press (2012). [Server]
	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, vol 3, 1186 (2012). [PDF] [Support Information]
	O.W. Nadeau, L.A. Lane, D. Xu, J. Sage, T.S. Priddy, A. Artigues, M. T. Villar, Q. Yang, C.V. Robinson, Y. Zhang and G.M. Carlson The Structure and Location of the Regulatory beta Subunits in the ([alpha][beta][gamma][delta])4 Phosphorylase Kinase Complex. Journal of Biological Chemistry, vol 287, 36651-36661 (2012). [PDF] [Commentary] [Best Paper of 2012 in JBC]
	Dong Xu, Yang Zhang Toward optimal fragment generations for ab initio protein structure assembly. Proteins: Structure, Function, and Bioinformatics, in press (2012).
	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, vol 80, 2311-2322 (2012). [PDF] [Support Information]
	Ambrish Roy, Yang Zhang Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure, vol 20, 987-997 (2012). [PDF] [Support Information] [Faculty of 1000]
	Ambrish Roy, Jianyi Yang, Yang Zhang COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, vol 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 interaction types exist in nature? PLoS One, vol 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, vol 80, 1715-1735 (2012). [PDF] [Support Information] [Server]
	Liu Hong, Xianghong Qi, Yang Zhang Dissecting the Kinetic Process of Amyloid Fiber Formation through Asymptotic Analysis. Journal of Physical Chemistry, vol 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, vol , 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, vol 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, vol 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, vol 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, vol 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, vol 19, 1784-1795 (2011). [PDF] [Support Information] [Commentary] [Server]
	Dong Xu, Yang Zhang Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization. Biophysical Journal, vol 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, vol 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, vol 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, vol 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, vol 57, e3259 (2011). [PDF] [Server] [Vedio]
	Sitao Wu, Andras Szilagyi, Yang Zhang Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions. Structure, vol 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, vol 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, vol 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, vol 5, 9-26 (2011). [PDF]
	Srayanta Mukherjee, Yang Zhang Protein-protein complex structure prediction by multimeric threading and template recombination. Structure, vol 19, 955-966 (2011). [PDF] [Support Information] [Server]
	Liu Hong, Xianghong Qi, Yang Zhang A lattice-gas model for amyloid fibril aggregation. Europhysics Letters, vol 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, vol 407, 764-776 (2011). [PDF] [Support Information]
2010
	Jian Zhang, Yang Zhang G protein-coupled receptor spatial restraint database for 3-D structure modeling and function annotation Bioinformatics. Bioinformatics, vol 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, vol 5, e15386 (2010). [PDF] [Server]
	Sitao Wu, Yang Zhang Recognizing Protein Substructure Similarity Using Segmental Threading. Structure, vol 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, vol 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, vol 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, vol 26, 889-895 (2010). [PDF] [Support Information] [Server]
2009
	Yang Zhang Protein structure prediction: when is it useful? Current Opinion in Structural Biology, vol 19, 145-155 (2009). [PDF]
	Srayanta Mukherjee, Yang Zhang MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Research, vol 37, e83 (2009). [PDF] [Support Information] [Server]
	Dong Xu, Yang Zhang Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS One, vol 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, vol 76, 665-676 (2009). [PDF] [Server]
	Yang Zhang I-TASSER: Fully automated protein structure prediction in CASP8. Proteins: Structure, Function, and Bioinformatics, vol 77 (Suppl 9), 100-113 (2009). [PDF] [Support Information]
	Yunqi Li, Ambrish Roy, Yang Zhang HAAD: An accurate algorithm for quickly predicting hydrogen positions in protein structures. PLoS One, vol 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, vol 10, 445 (2009). [PDF]
	Alper Kucukural, Andras Szilagyi, Ugur Sezerman, Yang Zhang Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism. 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, vol 18, 342-348 (2008). [PDF]
	Sitao Wu, Yang Zhang A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics, vol 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, vol 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, vol 72, 547-556 (2008). [PDF] [Server]
	Yang Zhang I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, vol 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, vol 16, 2716-2725 (2007). [PDF]
	Yang Zhang Template-based modeling and free modeling by I-TASSER in CASP7. Proteins: Structure, Function, and Bioinformatics, vol 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, vol 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, vol 5, 17 (2007). [PDF]
	Stephan Lorenzen, Yang Zhang Identification of near-native structures by clustering protein docking conformations. Proteins: Structure, Function, and Bioinformatics, vol 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, vol 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, vol 2, e13 (2006). [PDF]
	Vera Grimm, Yang Zhang, Jeffrey Skolnick Benchmarking of dimeric threading and structure refinement. Proteins: Structure, Function, and Bioinformatics, vol 63, 457-465 (2006). [PDF]
	Seung Yup Lee, Yang Zhang, Jeffrey Skolnick TASSER-based refinement of NMR structures. Proteins: Structure, Function, and Bioinformatics, vol 63, 451-456 (2006). [PDF]
	Haijun Zhou, Yang Zhang, Zhong-can Ou-Yang Theoretical and computational treatment 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, vol 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, vol 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, vol 102, 1029 (2005). [PDF] [Commentary]
	Haijun Zhou, Yang Zhang A Hierarchical Chain Model of Spider Capture Silk Elasticity. Physical Review Letters, vol 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, vol 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, vol 87, 2647 (2004). [PDF]
	Wei Li, Yang Zhang, Jeffrey Skolnick Application Of Sparse NMR Restraints To Large-Scale Protein Structure Prediction. Biophysical Journal, vol 87, 1241 (2004). [PDF]
	Yang Zhang, Jeffrey Skolnick Scoring Function for Automated Assessment of Protein Structure Template Quality. Proteins: Structure, Function, and Bioinformatics, vol 57, 702 (2004). [PDF] [Correction] [Server]
	Yang Zhang, Jeffery Skolnick SPICKER: A clustering approach to identify near-native protein folds. Journal of Computational Chemistry, vol 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, vol 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, vol 56, 502 (2004). [PDF]
	Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick Large-scale assessment of the utility of low resolution protein structures for biochemical assignment. Bioinformatics, vol 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, vol 53, 290 (2003). [PDF]
	Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick Touchstone II: A new approach to ab initio protein Structure Prediction. Biophysical Journal, vol 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, vol S53, 469-479 (2003). [PDF]
2002
	Haijun Zhou, Yang Zhang, Zhongcan Ouyang Elastic theories of single DNA molecules. Physica, vol 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, vol 99, 5993 (2002). [PDF]
	M. Dessinges, B. Maier, Yang Zhang, M. Peliti, D. Bensimon, V. Croquette Stretching ssDNA, a model polyelectrolyte. Physical Review Letters, vol 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, vol 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, vol 81, 1133 (2001). [PDF]
	Haijun Zhou, Yang Zhang Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter? Journal of Chemical Physics, vol 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, vol 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, vol 115, 5027 (2001). [PDF]
	Haijun Zhou, Yang Zhang, Zhongcan Ouyang Stretch-induced hairpin-coil transitions in designed polynucleotide chains. Physical Review Letters, vol 86, 356 (2001). [PDF]
2000
	Yang Zhang, Haijun Zhou, Zhongcan Ouyang Monte Carlo implementation of supercoiled double-stranded DNA. Biophysical Journal, vol 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, vol E62, 1045 (2000). [PDF]
	Yang Zhang Approach to Monte Carlo calculation of the buckling of supercoiled DNA loops. Physical Review, vol E62, RAPID COMMUNICATIONS, 5923 (2000). [PDF]
	Csaba Boros, Tachung Meng, Richard Rittel, Karsten Tabelow, Yang Zhang Formation of color-singlet gluon cluster and inelastic diffractive scattering. Physical Review, vol 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, vol 82, 2044 (1999). [PDF]
	Haijun Zhou, Yang Zhang, Zhongcan Ouyang Bending and Base-Stacking Interactions in Double-Stranded DNA. Physical Review Letters, vol 82, 4560 (1999). [PDF]