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TM-score TM-align US-align MM-align RNA-align NW-align LS-align EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot MR-REX I-TASSER-MR SVMSEQ NeBcon ResPRE TripletRes DeepPotential WDL-RF ATPbind DockRMSD DeepMSA FASPR EM-Refiner GPU-I-TASSER


Publications in Yang Zhang Lab

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Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang
US-align: Universal Structure Alignment of Proteins, Nucleic Acids and Macromolecular Complexes.
Nature Methods, in press (2022).
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, in press (2022).
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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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).
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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).
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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).
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).
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Xiaoqiong Wei, Chengxin Zhang, Peter L Freddolino, Yang Zhang
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons.
Bioinformatics, 36: 4383-4388 (2020).
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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).
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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).
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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).
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).
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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).
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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).
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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).
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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).
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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).
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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).
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]
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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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).
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).
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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).
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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).
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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).
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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]
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).
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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]
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).
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]
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).
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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).
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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]
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).
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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).
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).
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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]
Jeffrey R Brender, Yang Zhang
Protein–Protein Interactions and Genetic Disease.
Encyclopedia of Life Sciences, DOI: 10.1002/9780470015902.a0026856 (2017).
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.
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).
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).
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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).
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).
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).
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).
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).
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).
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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).
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Lijun Quan, Qiang Lv, Yang Zhang
STRUM: Structure-based prediction of protein stability changes upon single-point mutation.
Bioinformatics, 32: 2936-46 (2016).
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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).
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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).
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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).
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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).
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).
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).
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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).
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Haiyou Deng, Ya Jia, Yang Zhang
3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys.
Bioinformatics, 32: 378-87 (2016).
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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).
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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).
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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).
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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).
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).
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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).
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).
Jianyi Yang, Yang Zhang
I-TASSER server: new development for protein structure and function predictions.
Nucleic Acids Research, 43: W174-W181 (2015).
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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).
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).
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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).
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).
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Andras Szilagyi, Yang Zhang
Template-based structure modeling of protein-protein interactions.
Current Opinion in Structural Biology, 24: 10-23 (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, 3: 527-539 (2014).
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).
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).
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).
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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).
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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).
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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).
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Pralay Mitra, David Shultis, Yang Zhang
EvoDesign: de novo protein design based on structural and evolutionary profiles.
Nucleic Acids Research, 41: W273-W280 (2013).
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Zhiding Xue, Dong Xu, Yan Wang, Yang Zhang
ThreaDom: Extracting Protein Domain Boundary Information from Multiple Threading Alignments.
Bioinformatics, 29: i247-i256 (2013).
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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).
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).
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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).
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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).
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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).
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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).
Aysam Guerler, Brandon Govindarajoo, Yang Zhang
Mapping Monomeric Threading to Protein-Protein Structure Prediction.
Journal of Chemical Information and Modeling, 53: 717-725 (2013).
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Yang Zhang, Jeffrey Skolnick
Segment assembly, structure alignment and iterative simulation in protein structure prediction.
BMC Biology, 11: 44 (2013).
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).
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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).
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Dong Xu, Yang Zhang
Toward optimal fragment generations for ab initio protein structure assembly.
Proteins: Structure, Function, and Bioinformatics, 81: 229-239 (2013).
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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).
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Ambrish Roy, Yang Zhang
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement.
Structure, 20: 987-997 (2012).
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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).
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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).
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Ambrish Roy, Yang Zhang
Protein structure prediction.
Encyclopedia of Life Sciences, DOI: 10.1002/9780470015902.a0003031.pub2 (2012).
Ambrish Roy, Jianyi Yang, Yang Zhang
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation.
Nucleic Acids Research, 40: W471-W477 (2012).
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Leonardo Garma, Srayanta Mukherjee, Pralay Mitra, Yang Zhang
How many protein-protein interactions types exist in nature?
PLoS One, 7: e38913 (2012).
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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).
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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).
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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).
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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).
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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).
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).
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).
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Jian Zhang, Yu Liang, Yang Zhang
Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling.
Structure, 19: 1784-1795 (2011).
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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).
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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).
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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).
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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).
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).
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Sitao Wu, Andras Szilagyi, Yang Zhang
Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions.
Structure, 19: 1182-1191 (2011).
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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).
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).
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Srayanta Mukherjee, Yang Zhang
Protein-protein complex structure predictions by multimeric threading and template recombination.
Structure, 19: 955-966 (2011).
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Liu Hong, Xianghong Qi, Yang Zhang
A lattice-gas model for amyloid fibril aggregation.
Europhysics Letters, 94: 68006 (2011).
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).
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Jian Zhang, Yang Zhang
GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation.
Bioinformatics, 26: 3004-3005 (2010).
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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).
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Sitao Wu, Yang Zhang
Recognizing Protein Substructure Similarity Using Segmental Threading.
Structure, 18: 858-867 (2010).
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Ambrish Roy, Alper Kucukural, Yang Zhang
I-TASSER: a unified platform for automated protein structure and function prediction.
Nature Protocols, 5: 725-738 (2010).
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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.
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.
Jinrui Xu, Yang Zhang
How significant is a protein structure similarity with TM-score= 0.5?
Bioinformatics, 26: 889-895 (2010).
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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).
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Dong Xu, Yang Zhang
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.
PLoS One, 4: e8140 (2009).
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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.
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).
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Yang Zhang
I-TASSER: Fully automated protein structure prediction in CASP8.
Proteins: Structure, Function, and Bioinformatics, 77 (Suppl 9): 100-113 (2009).
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Yunqi Li, Ambrish Roy, Yang Zhang
HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.
PLoS One, 4: e6701 (2009).
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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.
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).
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.
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).
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Sitao Wu, Yang Zhang
ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction.
PLoS One, 3: e3400 (2008).
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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]
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).
Yang Zhang
Template-based modeling and free modeling by I-TASSER in CASP7.
Proteins: Structure, Function, and Bioinformatics, 69 (Suppl 8): 108-117 (2007).
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.
Sitao Wu, Yang Zhang
LOMETS: A local meta-threading-server for protein structure prediction.
Nucleic Acids Research, 35: 3375-3382 (2007).
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Sitao Wu, Jeffrey Skolnick, Yang Zhang
Ab initio modeling of small proteins by iterative TASSER simulations.
BMC Biology, 5: 17 (2007).
Stephan Lorenzen, Yang Zhang
Identification of near-native structures by clustering protein docking conformations.
Proteins: Structure, Function, and Bioinformatics, 68: 187-194 (2007).
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).
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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).
Vera Grimm, Yang Zhang, Jeffrey Skolnick
Benchmarking of dimeric threading and structure refinement.
Proteins: Structure, Function, and Bioinformatics, 63: 457-465 (2006).
Seung Yup Lee, Yang Zhang, Jeffrey Skolnick
TASSER-based refinement of NMR structures.
Proteins: Structure, Function, and Bioinformatics, 63: 451-456 (2006).
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.
Shashi Bhushan Pandit, Yang Zhang, Jeffrey Skolnick
TASSER-Lite: An Automated Tool for Protein Comparative Modeling.
Biophysical Journal, 91: 4180-4190 (2006).
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.
Yang Zhang, Jeffrey Skolnick
TM-align: a protein structure alignment algorithm based on the TM-score.
Nucleic Acids Research, 33: 2302-2309 (2005).
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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).
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).
Yang Zhang, Jeffrey Skolnick
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.
Biophysical Journal, 87: 2647 (2004).
Wei Li, Yang Zhang, Jeffrey Skolnick
Application Of Sparse NMR Restraints To Large-Scale Protein Structure Prediction.
Biophysical Journal, 87: 1241 (2004).
Yang Zhang, Jeffrey Skolnick
Scoring Function for Automated Assessment of Protein Structure Template Quality.
Proteins: Structure, Function, and Bioinformatics, 57: 702 (2004).
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Yang Zhang, Jeffery Skolnick
SPICKER: A clustering approach to identify near-native protein folds.
Journal of Computational Chemistry, 25: 865 (2004).
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).
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).
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).
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).
Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick
Touchstone II: A new approach to ab initio protein Structure Prediction.
Biophysical Journal, 85: 1145 (2003).
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).
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).
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).
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).
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).
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).
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
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