Publications in Yang Zhang Lab

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2023
	Yang Li, Chengxin Zhang, Chenjie Feng, Robin Pearce, Peter L. Freddolino, Yang Zhang Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction. Nature Communications, 14: 5745 (2023). [PDF] [Support Information] [Server]
	Robin Pearce, Xiaoqiang Huang, Gilbert S Omenn, Yang Zhang De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America, 120: e2208275120 (2023). [PDF] [Support Information] [Server]
2022
	Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang US-align: Universal Structure Alignment of Proteins, Nucleic Acids and Macromolecular Complexes. Nature Methods, 19: 195-204 (2022). [PDF] [Support Information] [Server]
	Robin Pearce, Yang Li, Gilbert S Omenn, Yang Zhang Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. PLOS Computational Biology, 18: e1010539 (2022). [PDF] [Support Information] [Server]
	Xiaogen Zhou, Wei Zheng, Yang Li, Robin Pearce, Chengxin Zhang, Eric W. Bell, Guijun Zhang, Yang Zhang I-TASSER-MTD: A deep-learning based platform for multi-domain protein structure and function prediction. Nature Protocols, 17: 2326-2353 (2022). [PDF] [Support Information] [Server]
	Haifeng Zhang, Renjie Shang, Kwantae Kim, Wei Zheng, Christopher J Johnson, Lei Sun, Xiang Niu, Liang Liu, Jingqi Zhou, Lingshu Liu, Zheng Zhang, Theodore A Uyeno, Jimin Pei, Skye D Fissette, Stephen A Green, Sukhada P Samudra, Junfei Wen, Jianli Zhang, Jonathan T Eggenschwiler, Douglas B Menke, Marianne E Bronner, Nick V Grishin, Weiming Li, Kaixiong Ye, Yang Zhang, Alberto Stolfi, Pengpeng Bi Evolution of a chordate-specific mechanism for myoblast fusion. Science Advances, 8: eadd2696 (2022). [PDF] [Support Information]
	Yang Li, Chengxin Zhang, Dong-Jun Yu, Yang Zhang Deep learning geometrical potential for high- accuracy ab initio protein structure prediction. iSciences, 25: 104425 (2022). [PDF] [Support Information] [Server]
	Yiheng Zhu, Chengxin Zhang, Yan Liu, Gilbert S Omenn, Peter L Freddolino, Dongjun Yu, Yang Zhang Integrating transcript expression profiles with protein homology inferences for gene function prediction. Genomics, Proteomics & Bioinformatics, 20: 1013-1027 (2022). [PDF] [Support Information] [Server]
	Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research, 50: W235-245 (2022). [PDF] [Support Information] [Server]
	Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nature Computational Science, 2: 265-275 (2022). [PDF] [Support Information] [Server]
	Yiheng Zhu, Chengxin Zhang, Dongjun Yu, Yang Zhang Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLOS Computational Biology, 18: e1010793 (2022). [PDF] [Support Information] [Server]
	Wallace Chan, Jiansheng Wu, Eric Bell, Yang Zhang Virtual Screening and Bioactivity Modeling for G Protein-Coupled Receptors. GPCRs as Therapeutic Targets, Chapter 12, Edited by Annette Gilchrist, (John Wiley & Sons, Inc., 2022), P. 388-423. [PDF]
	Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, Peter Freddolino, Yang Zhang LOMETS3: Integrating deep learning and profile-alignment for advanced protein template recognition and function annotation. Nucleic Acids Research, 50: W454-464 (2022). [PDF] [Support Information] [Server]
	Eric W Bell, Jacob H Schwartz, Peter L Freddolino, Yang Zhang PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. Journal of Molecular Biology, 434: 167530 (2022). [PDF] [Support Information] [Server]
	Harihar Milaganur Mohan, Hanna Trzeciakiewicz, Amit Pithadia, Emily V Crowley, Regina Pacitto, Nathaniel Safren, Bryce Trotter, Chengxin Zhang, Xiaogen Zhou, Yang Zhang, Venkatesha Basrur, Henry L Paulson, Lisa M Sharkey RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control. Cellular and Molecular Life Sciences, 79: 176 (2022). [PDF] [Support Information]
	Biao Zhang, Dong Liu, Yang Zhang, Hongbin Shen, Guijun Zhang Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning. Briefings in Bioinformatics, 23: bbac026 (2022). [PDF] [Support Information]
	Carlie A. LaLone, Donovan J. Blatz, Marissa A. Jensen, Sara M. F. Vliet, Sally Mayasich, Kali Z. Mattingly, Thomas R. Transue, Wilson Melendez, Audrey Wilkinson, Cody W. Simmons, Carla Ng, Chengxin Zhang, Yang Zhang From Protein Sequence to Structure: The Next Frontier in Cross-Species Extrapolation for Chemical Safety Evaluations. Environmental Toxicology and Chemistry, 42: 463-474 (2022). [PDF]
	Elijah A MacCarthy, Chengxin Zhang, Yang Zhang, Dukka KC GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. Bioinformatics, 38: 1754-1755 (2022). [PDF] [Support Information] [Server]
	Xi Zhang, Biao Zhang, Peter L Freddolino, Yang Zhang CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks. Nature Methods, 19: 195-204 (2022). [PDF] [Support Information] [Server]
2021
	S. M. Mortuza, Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Yang Zhang Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications, 12: 5011 (2021). [PDF] [Support Information] [Server]
	Pengshuo Yang, Wei Zheng, Kang Ning, Yang Zhang Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America, 118: e2110828118 (2021). [PDF] [Support Information]
	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1: 100014 (2021). [PDF] [Support Information] [Server]
	Robin Pearce, Yang Zhang Toward the solution of the protein structure prediction problem. Journal of Biological Chemistry, 297: 100870 (2021). [PDF] [This paper was recommended in Faculty Opinions]
	Wei Zheng, Yang Li, Chengxin Zhang, Xiaogen Zhou, Robin Pearce, Eric W Bell, Xiaoqiang Huang, Yang Zhang Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14. Proteins: Structure, Function, and Bioinformatics, 89: 1734-1751 (2021). [PDF] [Support Information]
	Yang Li, Chengxin Zhang, Wei Zheng, Xiaogen Zhou, Eric W Bell, Dong‐Jun Yu, Yang Zhang Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins: Structure, Function, and Bioinformatics, 89: 1911-1921 (2021). [PDF] [Support Information]
	Young-Tae Lee, Alex Ayoub, Sang-Ho Park, Liang Sha, Jing Xu, Fengbiao Mao, Wei Zheng, Yang Zhang, Uhn-Soo Cho, Yali Dou Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin. Nature Communications, 12: 2953 (2021). [PDF] [Support Information]
	Weikang Gong, Aysam Guerler, Chengxin Zhang, Elisa Warner, Chunhua Li, Yang Zhang Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology, 433: 166944 (2021). [PDF] [Support Information] [Server]
	Jaie Woodard, Chengxin Zhang, Yang Zhang ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities. Journal of Molecular Biology, 433: 166840 (2021). [PDF] [Database]
	Jaie Woodard, Wei Zheng, Yang Zhang Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PLoS Computational Biology, 17: e1009370 (2021). [PDF] [Support Information]
	Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dongjun Yu, Yang Zhang Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS Computational Biology, 17: e1008865 (2021). [PDF] [Support Information] [Server]
	Biao Zhang, Wenyi Zhang, Robin Pearce, Yang Zhang, Hongbin Shen Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. Journal of Physical Chemistry B, 125: 528-538 (2021). [PDF] [Support Information]
	Edison Ong, Xiaoqiang Huang, Robin Pearce, Yang Zhang, Yongqun He Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. Computational and Structural Biotechnology Journal, 19: 518-529 (2021). [PDF] [Support Information]
	Xiaoqiang Huang, Robin Pearce, Gilbert S Omenn, Yang Zhang Identification of 13 Guanidinobenzoyl-or Aminidinobenzoyl-Containing Drugs to Potentially Inhibit TMPRSS2 for COVID-19 Treatment. International journal of molecular sciences, 22: 7060 (2021). [PDF] [Support Information]
	Siqi Wu, Chang Tian, Panpan Liu, Dongjie Guo, Wei Zheng, Xiaoqiang Huang, Yang Zhang, Lijun Liu Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein–protein interactions. Journal of medical virology, 93: 2132-2140 (2021). [PDF] [Support Information]
	Sei Yoshida, Xiaoqiong Wei, Gensheng Zhang, Christopher L. O’Connor, Mauricio Torres, Zhangsen Zhou, Liangguang Lin, Rajasree Menon, Xiaoxi Xu, Wenyue Zheng, Yi Xiong, Edgar A. Otto, Chih-Hang Anthony Tang, Rui Hua, Rakesh Verma, Hiroyuki Mori, Yang Zhang, Chih-Chi Andrew Hu, Ming Liu, Puneet Garg, Jeffrey B. Hodgin, Shengyi Sun, Markus Bitzer, Ling Qi Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function. Journal of Clinical Investigation, 131: e143988 (2021). [PDF] [Support Information]
	Chengxin Zhang, Wei Zheng, Micah Cheng, Gilbert S. Omenn, Peter L. Freddolino, Yang Zhang Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of proteome research, 20: 1178-1189 (2021). [PDF] [Support Information]
	Kailong Zhao, Jun Liu, Xiaogen Zhou, Jianzhong Su, Yang Zhang, Guijun Zhang MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics, 37: 4350–4356 (2021).
	Md Saifur Rahman, Mst Hur Madina, Mélodie B Plourde, Karen Cristine Gonçalves dos Santos, Xiaoqiang Huang, Yang Zhang, Jean-François Laliberté, Hugo Germain The Fungal Effector Mlp37347 Alters Plasmodesmata Fluxes and Enhances Susceptibility to Pathogen. Microorganisms, 9: 1232 (2021). [PDF] [Support Information]
	Robin Pearce, Yang Zhang Deep learning techniques have significantly impacted protein structure prediction and protein design. Current Opinion in Structural Biology, 68: 194-207 (2021). [PDF]
2020
	Biao Zhang, Xi Zhang, Robin Pearce, Hongbin Shen, Yang Zhang A new protocol for atomic-level protein structure modeling and refinement using low-to-medium resolution cryo-EM density maps. Journal of Molecular Biology, 432: 5365-5377 (2020). [PDF] [Support Information] [Server]
	Wallace K.B. Chan, Yang Zhang Virtual screening of human Class-A GPCRs using ligand profiles built on multiple ligand-receptor interactions. Journal of Molecular Biology, 432: 4872-4890 (2020). [PDF] [Support Information] [Server]
	Xiaoqiang Huang, Chengxin Zhang, Robin Pearce, Gilbert S. Omenn, Yang Zhang Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2. Journal of Proteome Research, 19: 4844-4856 (2020). [PDF] [Support Information]
	Xiaoqiang Huang, Robin Pearce, Yang Zhang De novo design of protein peptides to block association of the SARS-CoV-2 spike protein with human ACE2. Aging, 12: 11263-11276 (2020). [PDF]
	Zhui Tu, Xiaoqiang Huang, Jinheng Fu, Na Hu, Wei Zheng, Yanping Li, Yang Zhang Landscape of Variable Domain of Heavy-chain-only Antibody Repertoire from Alpaca. Immunology, 161: 53-65 (2020). [PDF] [Support Information] [Database]
	Xiaoqiang Huang, Robin Pearce, Yang Zhang FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics, 36: 3758–3765 (2020). [PDF] [Support Information] [Server]
	Xiaoqiong Wei, Chengxin Zhang, Peter L Freddolino, Yang Zhang Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinformatics, 36: 4383-4388 (2020). [PDF] [Support Information] [Server]
	Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics, 36: 3749–3757 (2020). [PDF] [Support Information] [Server]
	Wenyi Zhang, Eric Bell, Minghao Yin, Yang Zhang EDock: Blind Protein-ligand Docking by Replica-Exchange Monte Carlo Simulation. Journal of Cheminformatics, 12: 37 (2020). [PDF] [Support Information] [Server]
	Stephanie S. Tseng-Rogenski, Koji Munakata, Daniel Y. Choi, Paul K. Martin, Supal Mehta, Minoru Koi, Wei Zheng, Yang Zhang, John M. Carethers The human DNA mismatch repair protein MSH3 contains nuclear localization and export signals that enable nuclear-cytosolic shuttling in response to inflammation. Molecular and Cellular Biology, 40: 00029-20 (2020). [PDF]
	Xiaoqiang Huang, Robin Pearce, Yang Zhang Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. Journal of Chemical Information and Modeling, 60: 410-420 (2020). [PDF] [Support Information]
	Chengxin Zhang, Wei Zheng, S. M. Mortuza, Yang Li, Yang Zhang DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics, 36: 2105-2112 (2020). [PDF] [Support Information 1, 2] [Server]
	Xiaoqiang Huang, Robin Pearce, Yang Zhang EvoEF2: Accurate and fast energy function for computational protein design. Bioinformatics, 36: 1135–1142 (2020). [PDF] [Support Information] [Server]
	Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics, 36: 2429-2437 (2020). [PDF] [Server]
	Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinformatics, 36: 751-757 (2020). [PDF] [Support Information] [Server]
	Yiheng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dongjun Yu Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings in Bioinformatics, 22: 1-14 (2020). [PDF] [Support Information]
	Di Wang, Ling Geng, Yujun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hongbin Shen Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinformatics, 36: 437-448 (2020). [PDF] [Support Information] [Server]
	Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, Guijun Zhang Underestimation-assisted global-local cooperative differential evolution and the application to protein structure prediction. IEEE Transactions on Evolutionary Computation, 24: 536-550 (2020). [PDF] [Support Information]
	Katelyn R. Soules, Aidan Dmitriev, Scott D. LaBrie, Zoë E. Dimond, Benjamin H. May, David K. Johnson, Yang Zhang, Kevin P. Battaile, Scott Lovell, P. Scott Hefty Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis supports role in TCA cycle regulation. Molecular Microbiology, 113: 68-88 (2020). [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, 19: 1351-1360 (2020). [PDF] [Support Information] [Database]
2019
	Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLOS Computational Biology, 15: e1007411 (2019). [PDF] [Support Information] [Server]
	Yan Wang, Qiang Shi, Pengshuo Yang, Chengxin Zhang, S. M. Mortuza, Zhidong Xue, Kang Ning, Yang Zhang Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. Genome Biology, 20: 229 (2019). [PDF] [Support Information 1, 2] [Database]
	Chengxin Zhang, Lydie Lane, Gilbert S. Omenn, Yang Zhang Blinded Testing of Function Annotation for uPE1 Proteins by the I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. Journal of Proteome Research, 18: 4154-4166 (2019). [PDF] [Support Information]
	Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, Yang Zhang Assembling multidomain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America, 116: 15930-15938 (2019). [PDF] [Support Information] [Server]
	Eric W. Bell, Yang Zhang DockRMSD: an Open-Source Tool for Atom Mapping and RMSD Calculation of Symmetric Molecules through Graph Isomorphism. Journal of Cheminformatics, 11: 40 (2019). [PDF] [Server]
	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, 87: 1082-1091 (2019). [PDF] [Support Information]
	Wei Zheng, Yang Li, Chengxin Zhang, Robin Pearce, S. M. Mortuza, Yang Zhang Deep-learning contact-map guided protein structure prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, 87: 1149-1164 (2019). [PDF] [Support Information]
	Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang LOMETS2: Improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Research, 47: W429-W436 (2019). [PDF] [Support Information] [Server]
	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, 35: 4647-4655 (2019). [PDF] [Support Information] [Server]
	Heedoo Lee, Chunhua Li, Yang Zhang, Duo Zhang, Leo E. Otterbein, Yang Jin Caveolin-1 selectively regulates microRNA sorting into microvesicles after noxious stimuli. Journal of Experimental Medicine, 216: 2202-2220 (2019). [PDF] [Support Information]
	Jiansheng Wu, Ben Liu, Wallace K.B. Chan, Weijian Wu, Tao Pang, Haifeng Hu, Shancheng Yan, Xiaoyan Ke, Yang Zhang Precise Modelling and Interpretation of Bioactivities of Ligands Targeting G Protein-coupled Receptors. Bioinformatics, 35: i324-i332 (2019). [PDF] [Support Information] [Server]
	Robin Pearce, Xiaoqiang Huang, Dani Setiawan, Yang Zhang EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function. Journal of Molecular Biology, 431: 2467-2476 (2019). [PDF] [Support Information] [Server]
	Sang Ho Park, Alex Ayoub, Young-Tae Lee, Jing Xu, Hanseong Kim, Wei Zheng, Biao Zhang, Liang Sha, Sojin An, Yang Zhang, Michael A Cianfrocco, Min Su, Yali Dou, Uhn-Soo Cho Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nature Communications, 10: 5540 (2019). [PDF] [Support Information]
	Wei Zheng, Chengxin Zhang, Eric W Bell, Yang Zhang I-TASSER Gateway: A Protein Structure and Function Prediction Server Powered by XSEDE. Future Generation Computer Systems, 99: 73-85 (2019). [PDF]
	Abdul Basit, Saima Sadaf, Yang Zhang, M. Waheed Akhtar Improvement in activity of cellulase Cel12A of Thermotoga neapolitana by the error prone PCR. Journal of Biotechnology, 306: 118-124 (2019). [PDF]
	Zhongjie Han, Qi Shao, Weikang Gong, Shihao Wang, Jiguo Su, Chunhua Li, Yang Zhang Interpreting the dynamics of binding interactions of snRNA and U1A using a coarse-grained model. Biophysical Journal, 116: 1625-1636 (2019). [PDF] [Support Information]
	David Shultis, Pralay Mitra, Xiaoqiang Huang, Jarrett Johnson, Naureen Aslam Khattak, Felicia Gray, Clint Piper, Jeff Czajka, Logan Hansen, Bingbing Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, Jeanne Stuckey, Tomasz Cierpicki, Christoph H. Borchers, Shaomeng Wang, Ming Lei, Yang Zhang Changing the Apoptosis Pathway through Evolutionary Protein Design. Journal of Molecular Biology, 431: 825-841 (2019). [PDF] [Support Information]
	Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh, Alex W Crocker, Kimberley A Lewis, George Georghiou, Huy N Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L Hurto, Peter L Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M Fernández, Branislava Gemovic, Vladimir R Perovic, Radoslav S Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad RK Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A Freitas, Magdalena Antczak, Fabio Fabris, Mark N Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J Medlar, Zosa The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome biology, 20: 244 (2019). [PDF] [Support Information]
	Lijun Quan, Hongjie Wu, Qiang Lyu, Yang Zhang DAMpred: Recognizing disease-associated nsSNPs through Bayes-guided neural-network model built on low-resolution structure prediction of proteins and protein-protein interactions. Journal of Molecular Biology, 431: 2449-2459 (2019). [PDF] [Support Information] [Server]
	Sha Gong, Chengxin Zhang, Yang Zhang RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinformatics, 35: 4459-4461 (2019). [PDF] [Correction] [Server]
2018
	Jouko J. Virtanen, Yang Zhang MR-REX: Molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models. Acta Crystallographica Section D, 74: 606-620 (2018). [PDF] [Support Information] [Server]
	Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Journal of Molecular Biology, 430: 2256-2265 (2018). [PDF] [Support Information] [Server]
	Chengxin Zhang, Xiaoqiong Wei, Gilbert S. Omenn, Yang Zhang Structure and Protein Interaction-based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. Journal of Proteome Research, 17: 4186-4196 (2018). [PDF] [Support Information] [Database]
	Dani Setiawan, Jeffrey R Brender, Yang Zhang Recent Advances in Automated Protein Design and Its Future Challenges. Expert Opinion On Drug Discovery, 13: 587-604 (2018). [PDF]
	Jiansheng Wu, Qiuming Zhang, Weijian Wu, Tao Pang, Haifeng Hu, Wallace K.B. Chan, Xiaoyan Ke, Yang Zhang WDL-RF: Predicting Bioactivities of Ligand Molecules Acting with G Protein-coupled Receptors by Combining Weighted Deep Learning and Random Forest. Bioinformatics, 34: 2271-2282 (2018). [PDF] [Support Information] [Server]
	Runze Dong, Zhenling Peng, Yang Zhang, Jianyi Yang mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics, 34: 1719-1725 (2018). [PDF] [Support Information] [Server]
	Jun Hu, Zi Liu, Dongjun Yu, Yang Zhang LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinformatics, 34: 2209-2218 (2018). [PDF] [Support Information] [Server]
	Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang mTM-align: a server for fast protein structure database search and multiple protein structure alignment. Nucleic Acids Research, 46: W380-W386 (2018). [PDF] [Support Information] [Server]
	Chunqiu Xia, Ke Han, Yong Qi, Yang Zhang, Dongjun Yu A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15: 1315-1324 (2018). [PDF] [Support Information]
	Chen Keasar, Liam J. McGuffin, Björn Wallner, Badri Adhikari, Minkyung Baek, Debswapna Bhattacharya, Lauren Blake, Leandro Bortot, Renzhi Cao, Gaurav Chopra, Balakrishnan K. Dhanasekaran, Itzhel Dimas, Rodrigo Faccioli, Eshel Faraggi, Sambit Ghosh, Soma Ghosh, Lulasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milos Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergei Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yan P. Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Robert Ganzynkowicz, Artur Giełdoń, Brian Koepnick, Zoran Popović, Magdalena Ślusarz, Rafal Ślusarz, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Delbem, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söeding, Saraswathi Vishveshwara, Dong Xu, Foldit Players, Silvia N. Crivelli An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports, 8: 9939 (2018). [PDF]
	Jun Hu, Yang Li, Yang Zhang, Dongjun Yu ATPbind: accurate protein-ATP binding site prediction by combining sequence-profiling and structure-based comparisons. Journal of Chemical Information and Modeling, 58: 501-510 (2018). [PDF] [Support Information] [Server]
	Qi Wu, Zhenling Peng, Yang Zhang, Jianyi Yang COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Research, 46: W438-W442 (2018). [PDF] [Support Information] [Server]
	Chengxin Zhang, S M Mortuza, Baoji He, Yanting Wang, Yang Zhang Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins: Structure, Function, and Bioinformatics, 86 (Suppl 1): 136-151 (2018). [PDF] [Support Information]
2017
	Jeffrey R Brender, Yang Zhang Protein–Protein Interactions and Genetic Disease. Encyclopedia of Life Sciences, DOI: 10.1002/9780470015902.a0026856 (2017). [PDF]
	Yan Wang, Jouko Virtanen, Zhidong Xue, Yang Zhang I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. Nucleic Acids Research, 45: W429-434 (2017). [PDF] [Server]
	Jooyoung Lee, Peter Freddolino, Yang Zhang Ab initio protein structure prediction. From Protein Structure to Function with Bioinformatics, Chapter 1, Edited by D. J. Rigden, (Springer-London, 2017), P. 3-35. [PDF]
	Tao Xu, Sung‐Soo Park, Benedetto Daniele Giaimo, Daniel Hall, Francesca Ferrante, Diana M Ho, Kazuya Hori, Lucas Anhezini, Iris Ertl, Marek Bartkuhn, Honglai Zhang, Eléna Milon, Kimberly Ha, Kevin P Conlon, Rork Kuick, Brandon Govindarajoo, Yang Zhang, Yuqing Sun, Yali Dou, Venkatesha Basrur, Kojo SJ Elenitoba‐Johnson, Alexey I Nesvizhskii, Julian Ceron, Cheng‐Yu Lee, Tilman Borggrefe, Rhett A Kovall, Jean‐François Rual RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. EMBO Journal, 36: 3232-3249 (2017). [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, 45: W291-299 (2017). [PDF] [Support Information] [Server]
	Gustavo Glusman, Peter W. Rose, Andreas Prlić, Jennifer Dougherty, José M. Duarte, Andrew S. Hoffman,Geoffrey J. Barton, Emøke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan, Stephen K. Burley, Binghuang Cai, Hannah Carter, JianJiong Gao, Adam Godzik, Michael Heuer, Michael Hicks, Thomas Hrabe, Rachel Karchin, Julia Koehler Leman, Lydie Lane, David L Masica, Sean D Mooney, John Moult, Gilbert S Omenn, Frances Pearl, Vikas Pejaver, Sheila M. Reynolds, Ariel Rokem, Torsten Schwede, Sicheng Song, Hagen Tilgner, Yana Valasatava, Yang Zhang, Eric W. Deutsch Mapping genetic variations to threedimensional protein structures to enhance variant interpretation: a proposed framework. Genome Medicine, 9: 113 (2017). [PDF]
	Mary Ashley Rimmer, Owen W. Nadeau, Jianyi Yang, Antonio Artigues, Yang Zhang, Gerald M. Carlson The Structure of the Large Regulatory α Subunit of Phosphorylase Kinase Examined by Modeling and Hydrogen-Deuterium Exchange. Protein Science, 27: 472-484 (2017). [PDF]
	Hongdong Li, Yang Zhang, Yuanfang Guan, Rajasree Menon, Gilbert S. Omenn Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. Methods in Molecular Biology, 1558: 415-436 (2017). [PDF]
	Jens M. H. Thomas, Felix Simkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang, Daniel J. Rigdena Approaches to ab initio molecular replacement of a-helical transmembrane proteins. Acta Crystallographica Section D, 73: 985-996 (2017). [PDF]
	Yan Wang, Jian Wang, Ruiming Li, Qiang Shi, Zhidong Xue, Yang Zhang ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Research, 45: W400-407 (2017). [PDF] [Server]
	Ismaila O. Nurain, Clement O. Bewaji, Jarrett S. Johnson, Robertson D. Davenport, Yang Zhang Potential of Three Ethnomedicinal Plants as Antisickling Agents. Molecular Pharmaceutics, 14: 172-182 (2017). [PDF]
	Baoji He, S. M. Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang NeBcon: Protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinformatics, 33: 2296-2306 (2017). [PDF] [Support Information] [Server]
	Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang BindProfX: Assessing mutation-induced binding affinity change by protein interface profiles with pseudo counts. Journal of Molecular Biology, 429: 426-434 (2017). [PDF] [Support Information] [Server]
2016
	Lijun Quan, Qiang Lv, Yang Zhang STRUM: Structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics, 32: 2936-46 (2016). [PDF] [Support Information] [Server]
	Yan Wang, Jouko Virtanen, Zhidong Xue, John J. G. Tesmer, Yang Zhang Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallographica Section D, 72: 616-28 (2016). [PDF] [Support Information] [Server]
	Xiuzhen Hu, Qiwen Dong, Jianyi Yang, Yang Zhang Recognizing metal and acid radical ion binding sites by integrating ab initio modeling with template-based transferals. Bioinformatics, 32: 3260-3269 (2016). [PDF] [Support Information] [Server]
	Chunhua Li, Dashuai Lv, Lei Zhang, Feng Yang, Cunxin Wang, Jiguo Su, Yang Zhang Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model. Journal of Chemical Physics, 145: 014104 (2016). [PDF] [Support Information]
	Jeffrey R. Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang An Evolution Based Approach to de novo Protein Design. Methods in Molecular Biology, 1529: 243-264 (2016). [PDF]
	Jianyi Yang, Wenxuan Zhang, Baoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hong-Bin Shen, Yang Zhang Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins: Structure, Function, and Bioinformatics, 84 (Suppl 1): 233-246 (2016). [PDF]
	Wenxuan Zhang, Jianyi Yang, Baoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hong-Bin Shen, Yang Zhang Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11. Proteins: Structure, Function, and Bioinformatics, 84 (Suppl 1): 76-86 (2016). [PDF] [Support Information]
	Hong-Dong Li, Rajasree Menon, Ridvan Eksi, Aysam Guerler, Yang Zhang, Gilbert S. Omenn, Yuanfang Guan A Network of Splice Isoforms for the Mouse. Scientific Reports, 6: 24507 (2016). [PDF] [Support Information]
	Haiyou Deng, Ya Jia, Yang Zhang 3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys. Bioinformatics, 32: 378-87 (2016). [PDF] [Support Information] [Server]
	Jianyi Yang, Yan Wang, Yang Zhang ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction. Journal of Molecular Biology, 428: 693-701 (2016). [PDF] [Support Information] [Server]
2015
	Jeffrey R. Brender, Yang Zhang Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. PLOS Computational Biology, 11: e1004494 (2015). [PDF] [Support Information] [Server]
	Qiwen Dong, Rajasree Menon, Gilbert S. Omenn, Yang Zhang Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. Journal of Proteome Research, 14: 3750-3761 (2015). [PDF] [Database]
	Jing Yang, Baoji He, Richard Jang, Yang Zhang, Hongbin Shen Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins. Bioinformatics, 31: 3773-3781 (2015). [PDF] [Support Information] [Server]
	Jianyi Yang, Yang Zhang Protein Structure and Function Prediction Using I-TASSER. Current Protocols in Bioinformatics, 52: 5.8.1-5.8.15 (2015). [PDF] [Server]
	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, 23: 1538-1549 (2015). [PDF] [Support Information] [Server] [Database] [MasterClass—Dos, Don'ts, and How-Tos with Yang Zhang: Biology in 3D]
	David Shultis, Gregory Dodge, Yang Zhang Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering. Journal of Structural Biology, 191: 197-206 (2015). [PDF]
	Wallace Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey Brender, Junguk Hur, Arzucan Ozgur, Yang Zhang GLASS: a comprehensive database for experimentally-validated GPCR-ligand associations. Bioinformatics, 31: 3035-3042 (2015). [PDF] [Support Information] [Database]
	Hongdong Li, Rajasree Menon, Brandon Govindarajoo, Bharat Panwar, Yang Zhang, Gilbert S Omenn, Yuanfang Guan Functional Networks of Highest-Connected Splice Isoforms, from the Chromosome 17 Human Proteome Project. Journal of Proteome Research, 14: 3484-3491 (2015). [PDF]
	Richard Jang, Yan Wang, Zhidong Xue, Yang Zhang NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment. Journal of Biomolecular NMR, 62: 511-525 (2015). [PDF]
	Jianyi Yang, Yang Zhang I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Research, 43: W174-W181 (2015). [PDF] [Support Information] [Server]
	Haiping Sun, Yan Huang, Xiaofan Wang, Yang Zhang, Hongbin Shen Improving accuracy of protein contact prediction using balanced network deconvolution. Proteins: Structure, Function, and Bioinformatics, 83: 485-496 (2015). [PDF] [Server]
	Hongying Du, Jeffrey R Brender, Jian Zhang, Yang Zhang Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening. Methods, 71: 77-84 (2015). [PDF]
	Yingying Xu, Fan Yang, Yang Zhang, Hongbin Shen Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. Bioinformatics, 31: 1111-1119 (2015). [PDF] [Support Information]
	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, D71: 338-343 (2015). [PDF]
	Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8 (2015). [PDF] [Support Information] [Server]
2014
	Andras Szilagyi, Yang Zhang Template-based structure modeling of protein-protein interactions. Current Opinion in Structural Biology, 24: 10-23 (2014). [PDF]
	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, 3: 527-539 (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 (Suppl 2): 175-187 (2014). [PDF] [Support Information]
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]
	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. 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 contacts 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 localization predictor (iLocator) reveals protein mislocalizations in cancer tissues. Bioinformatics, 29: 2032-2040 (2013). [PDF] [Support Information] [Server]
	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]
	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, Stephen G. Waxman 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, Yang Zhang Protein structure prediction. Encyclopedia of Life Sciences, DOI: 10.1002/9780470015902.a0003031.pub2 (2012). [PDF]
	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]
	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]
	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]
	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 the United States of America, 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: 2302-2309 (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 the United States of America, 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 the United States of America, 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
	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 the United States of America, 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, 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]
	Haijun Zhou, Yang Zhang, Zhongcan Ouyang Stretch-induced hairpin-coil transitions in designed polynucleotide chains. Physical Review Letters, 86: 356 (2001). [PDF]