Most Cited Publications in Yang Zhang Lab
( Google Scholar Citation of Zhang Lab Publications)
Articles with more than 1000 citations
- 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]
- Yang Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, vol 9, 40 (2008). [PDF]
- Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, vol 12, 7-8 (2015). [PDF] [Support Information]
- Yang Zhang, Jeffrey Skolnick. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research, vol 33, 2302 (2005). [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]
- Jianyi Yang, Yang Zhang. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Research, vol 43, W174-W181 (2015). [PDF] [Support Information]
Articles with more than 500 citations
- 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]
- 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]
- 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]
- Jianyi Yang, Ambrish Roy, Yang Zhang. Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, vol 29, 2588 (2013). [PDF] [Support Information]
- 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]
- 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]
- Yang Zhang. Progress and challenges in protein structure prediction. Current Opinion in Structural Biology, vol 18, 342-348 (2008). [PDF]
- Sitao Wu, Jeffrey Skolnick, Yang Zhang. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biology, vol 5, 17 (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]
Articles with more than 200 citations
- 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]
- 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. 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]
- 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]
- 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]
- Jianyi Yang, Yang Zhang. Protein Structure and Function Prediction Using I-TASSER. Current Protocols in Bioinformatics, vol 52, 5.8.1-5.8.15 (2015). [PDF]
- Chengxin Zhang, Peter L. Freddolino, Yang Zhang. COFACTOR: improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Nucleic Acids Research, vol 45, W291-299 (2017). [PDF] [Support Information]
- Yang Zhang. Protein structure prediction: when is it useful? Current Opinion in Structural Biology, vol 19, 145-155 (2009). [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]
- 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]
- 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]
- 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]
- Chengxin Zhang, Wei Zheng, Xiaoqiang Huang, Eric W Bell, Xiaogen Zhou, Yang Zhang. Protein structure and sequence re-analysis of 2019-nCoV genome refutes snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1. Journal of proteome research, vol 19, 1351-1360 (2020). [PDF] [Support Information]
- Lijun Quan, Qiang Lv, Yang Zhang. STRUM: Structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics, vol 32, 2936-46 (2016). [PDF] [Support Information]
- 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]
- M. Dessinges, B. Maier, Yang Zhang, M. Peliti, D. Bensimon, V. Croquette. Stretching single stranded DNA, a model polyelectrolyte. Physical Review Letters, vol 89, 248102 (2002). [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]
- Jooyoung Lee, Peter Freddolino, Yang Zhang. Ab initio protein structure prediction. From Protein Structure to Function with Bioinformatics, vol , 3-35 (2017). [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]
- 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]
- Dong Xu, Yang Zhang. Toward optimal fragment generations for ab initio protein structure assembly. Proteins: Structure, Function, and Bioinformatics, vol 81, 229-239 (2013). [PDF] [Support Information]
Articles with more than 100 citations
- 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]
- 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, vol 3, 2619 (2013). [PDF] [Support Information]
- 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, 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]
- Srayanta Mukherjee, Yang Zhang. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure, vol 19, 955-966 (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]
- Andras Szilagyi, Yang Zhang. Template-based structure modeling of protein-protein interactions. Current Opinion in Structural Biology, vol 24, 10-23 (2014). [PDF]
- Jian Zhang, Jianyi Yang, Richard Jang, Yang Zhang. GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure, vol 23, 1538-1549 (2015). [PDF] [Support Information]
- Dong Xu, Yang Zhang. Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS One, vol 4, e8140 (2009). [PDF]
- Haijun Zhou, Yang Zhang, Zhongcan Ouyang. Bending and Base-Stacking Interactions in Double-Stranded DNA. Physical Review Letters, vol 82, 4560 (1999). [PDF]
- Yang Li, Chengxin Zhang, Eric W. Bell, Dongjun Yu, Yang Zhang. Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, vol 87, 1082-1091 (2019). [PDF] [Support Information]
- 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]
- Jeffrey R. Brender, Yang Zhang. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. PLOS Computational Biology, vol 11, e1004494 (2015). [PDF] [Support Information]
- Yang Zhang. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10. Proteins: Structure, Function, and Bioinformatics, vol 82, 175-187 (2014). [PDF] [Support Information]
- Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang. ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinformatics, vol 35, 4647-4655 (2019). [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]
- Yang Zhang, Jeffrey Skolnick. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophysical Journal, vol 87, 2647 (2004). [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]