Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. - Adrian K. Arakaki; Yang Zhang 040; Jeffrey Skolnick (Bioinform., 2004)

SPICKER: A clustering approach to identify near-native protein folds. - Yang Zhang 040; Jeffrey Skolnick (J. Comput. Chem., 2004)

Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. - Yang Zhang 040; Mark E. DeVries; Jeffrey Skolnick (PLoS Comput. Biol., 2006)

Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. - Yang Zhang 040; Mark E. DeVries; Jeffrey Skolnick (PLoS Comput. Biol., 2006)

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. - Sitao Wu; Yang Zhang 040 (Bioinform., 2008)

I-TASSER server for protein 3D structure prediction. - Yang Zhang 040 (BMC Bioinform., 2008)

How significant is a protein structure similarity with TM-score = 0.5? - Jinrui Xu; Yang Zhang 040 (Bioinform., 2010)

GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation. - Jian Zhang; Yang Zhang 040 (Bioinform., 2010)

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. - Ambrish Roy; Jianyi Yang 002; Yang Zhang 040 (Nucleic Acids Res., 2012)

Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. - Dong Xu 008; Hua Li 009; Yang Zhang 040 (RECOMB, 2013)

An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues. - Ying-Ying Xu; Fan Yang; Yang Zhang 040; Hong-Bin Shen (Bioinform., 2013)

ThreaDom: extracting protein domain boundary information from multiple threading alignments. - Zhidong Xue; Dong Xu; Yan Wang; Yang Zhang 040 (Bioinform., 2013)

High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. - Jing Yang; Richard Jang; Yang Zhang 040; Hong-Bin Shen (Bioinform., 2013)

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. - Jianyi Yang 002; Ambrish Roy; Yang Zhang 040 (Bioinform., 2013)

Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition. - Dong Xu 008; Hua Li 009; Yang Zhang 040 (J. Comput. Biol., 2013)

Mapping Monomeric Threading to Protein-Protein Structure Prediction. - Aysam Guerler; Brandon Govindarajoo; Yang Zhang 040 (J. Chem. Inf. Model., 2013)

EvoDesign: de novo protein design based on structural and evolutionary profiles. - Pralay Mitra; David Shultis; Yang Zhang 040 (Nucleic Acids Res., 2013)

BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. - Jianyi Yang 002; Ambrish Roy; Yang Zhang 040 (Nucleic Acids Res., 2013)

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis. - Pralay Mitra; David Shultis; Jeffrey R. Brender; Jeff Czajka; David Marsh; Felicia Gray; Tomasz Cierpicki; Yang Zhang 040 (PLoS Comput. Biol., 2013)

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. - Wallace K. B. Chan; Hongjiu Zhang; Jianyi Yang 002; Jeffrey R. Brender; Junguk Hur; Arzucan Özgür; Yang Zhang 040 (Bioinform., 2015)

Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. - Ying-Ying Xu; Fan Yang; Yang Zhang 040; Hong-Bin Shen (Bioinform., 2015)

Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins. - Jing Yang; Bao-Ji He; Richard Jang; Yang Zhang 040; Hong-Bin Shen (Bioinform., 2015)

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. - Shanshan Cheng; Yang Zhang 040; Charles L. Brooks III (BMC Bioinform., 2015)

I-TASSER server: new development for protein structure and function predictions. - Jianyi Yang 002; Yang Zhang 040 (Nucleic Acids Res., 2015)

Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. - Jeffrey R. Brender; Yang Zhang 040 (PLoS Comput. Biol., 2015)

3DRobot: automated generation of diverse and well-packed protein structure decoys. - Haiyou Deng; Ya Jia; Yang Zhang 040 (Bioinform., 2016)

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. - Xiuzhen Hu; Qiwen Dong; Jianyi Yang 002; Yang Zhang 040 (Bioinform., 2016)

STRUM: structure-based prediction of protein stability changes upon single-point mutation. - Lijun Quan; Qiang Lv; Yang Zhang 040 (Bioinform., 2016)

NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers. - Baoji He; S. M. Mortuza; Yanting Wang; Hong-Bin Shen; Yang Zhang 040 (Bioinform., 2017)

I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. - Yan Wang; Jouko Virtanen; Zhidong Xue; Yang Zhang 040 (Nucleic Acids Res., 2017)

ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. - Yan Wang; Jian Wang; Ruiming Li; Qiang Shi; Zhidong Xue; Yang Zhang 040 (Nucleic Acids Res., 2017)

COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. - Chengxin Zhang; Peter L. Freddolino; Yang Zhang 040 (Nucleic Acids Res., 2017)

THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. - Justin S. Diamond; Yang Zhang 040 (Database J. Biol. Databases Curation, 2018)

mTM-align: an algorithm for fast and accurate multiple protein structure alignment. - Runze Dong; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Bioinform., 2018)

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. - Jun Hu 011; Zi Liu; Dong-Jun Yu; Yang Zhang 040 (Bioinform., 2018)

WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. - Jiansheng Wu; Qiuming Zhang; Weijian Wu; Tao Pang; Haifeng Hu 004; Wallace K. B. Chan; Xiaoyan Ke; Yang Zhang 040 (Bioinform., 2018)

ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. - Jun Hu 011; Yang Li 107; Yang Zhang 040; Dong-Jun Yu (J. Chem. Inf. Model., 2018)

mTM-align: a server for fast protein structure database search and multiple protein structure alignment. - Runze Dong; Shuo Pan; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Nucleic Acids Res., 2018)

COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. - Qi Wu 016; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Nucleic Acids Res., 2018)

A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data. - Chun-Qiu Xia; Ke Han; Yong Qi; Yang Zhang 040; Dong-Jun Yu (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. - Sha Gong; Chengxin Zhang; Yang Zhang 040 (Bioinform., 2019)

ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. - Yang Li 107; Jun Hu 011; Chengxin Zhang; Dong-Jun Yu; Yang Zhang 040 (Bioinform., 2019)

Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors. - Jiansheng Wu; Ben Liu; Wallace K. B. Chan; Weijian Wu; Tao Pang; Haifeng Hu 004; Shancheng Yan; Xiaoyan Ke; Yang Zhang 040 (Bioinform., 2019)

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. - Wei Zheng 013; Chengxin Zhang; Eric W. Bell; Yang Zhang 040 (Future Gener. Comput. Syst., 2019)

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. - Eric W. Bell; Yang Zhang 040 (J. Cheminformatics, 2019)

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. - Wei Zheng 013; Chengxin Zhang; Qiqige Wuyun; Robin Pearce; Yang Li 107; Yang Zhang 040 (Nucleic Acids Res., 2019)

Detecting distant-homology protein structures by aligning deep neural-network based contact maps. - Wei Zheng 013; Qiqige Wuyun; Yang Li 107; S. M. Mortuza; Chengxin Zhang; Robin Pearce; Jishou Ruan; Yang Zhang 040 (PLoS Comput. Biol., 2019)

FASPR: an open-source tool for fast and accurate protein side-chain packing. - Xiaoqiang Huang; Robin Pearce; Yang Zhang 040 (Bioinform., 2020)

EvoEF2: accurate and fast energy function for computational protein design. - Xiaoqiang Huang; Robin Pearce; Yang Zhang 040 (Bioinform., 2020)

SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. - Xiaoqiang Huang; Wei Zheng 013; Robin Pearce; Yang Zhang 040 (Bioinform., 2020)

CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. - Jun Liu 078; Xiao-Gen Zhou; Yang Zhang 040; Gui-Jun Zhang (Bioinform., 2020)

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. - Sweta Vangaveti; Thom Vreven; Yang Zhang 040; Zhiping Weng (Bioinform., 2020)

Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. - Di Wang; Ling Geng; Yu-Jun Zhao; Yang Yang 030; Yan Huang; Yang Zhang 040; Hong-Bin Shen (Bioinform., 2020)

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. - Xiaoqiong Wei; Chengxin Zhang; Peter L. Freddolino; Yang Zhang 040; Zhiyong Lu (Bioinform., 2020)

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. - Chengxin Zhang; Wei Zheng 013; S. M. Mortuza; Yang Li 107; Yang Zhang 040 (Bioinform., 2020)

FUpred: detecting protein domains through deep-learning-based contact map prediction. - Wei Zheng 013; Xiaogen Zhou; Qiqige Wuyun; Robin Pearce; Yang Li 107; Yang Zhang 040 (Bioinform., 2020)

EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. - Wenyi Zhang 003; Eric W. Bell; Minghao Yin; Yang Zhang 040 (J. Cheminformatics, 2020)

Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. - Xiaoqiang Huang; Robin Pearce; Yang Zhang 040 (J. Chem. Inf. Model., 2020)

Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction. - Xiaogen Zhou; Chunxiang Peng; Jun Liu 078; Yang Zhang 040; Gui-Jun Zhang (IEEE Trans. Evol. Comput., 2020)

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. - Yi-Heng Zhu 001; Jun Hu 010; Fang Ge; Fuyi Li; Jiangning Song; Yang Zhang 040; Dong-Jun Yu (Briefings Bioinform., 2021)

MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. - Kai-Long Zhao; Jun Liu 078; Xiao-Gen Zhou; Jianzhong Su; Yang Zhang 040; Gui-Jun Zhang (Bioinform., 2021)

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. - Yang Li 107; Chengxin Zhang; Eric W. Bell; Wei Zheng 013; Xiaogen Zhou; Dong-Jun Yu; Yang Zhang 040 (PLoS Comput. Biol., 2021)

Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. - Jaie C. Woodard; Wei Zheng 013; Yang Zhang 040 (PLoS Comput. Biol., 2021)

Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning. - Biao Zhang; Dong Liu; Yang Zhang 040; Hong-Bin Shen; Gui-Jun Zhang (Briefings Bioinform., 2022)

GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. - Elijah A. MacCarthy; Chengxin Zhang; Yang Zhang 040; Dukka B. KC (Bioinform., 2022)

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. - Wei Zheng 013; Qiqige Wuyun; Xiaogen Zhou; Yang Li 107; Peter L. Freddolino; Yang Zhang 040 (Nucleic Acids Res., 2022)

DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. - Xiaogen Zhou; Chunxiang Peng; Wei Zheng 013; Yang Li 107; Guijun Zhang; Yang Zhang 040 (Nucleic Acids Res., 2022)

Progressive assembly of multi-domain protein structures from cryo-EM density maps. - Xiaogen Zhou; Yang Li 107; Chengxin Zhang; Wei Zheng 013; Guijun Zhang; Yang Zhang 040 (Nat. Comput. Sci., 2022)

Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. - Robin Pearce; Yang Li 107; Gilbert S. Omenn; Yang Zhang 040 (PLoS Comput. Biol., 2022)

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. - Yi-Heng Zhu 001; Chengxin Zhang; Yan Liu 038; Gilbert S. Omenn; Peter L. Freddolino; Dong-Jun Yu; Yang Zhang 040 (Genom. Proteom. Bioinform., 2022)

Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. - Yi-Heng Zhu 001; Chengxin Zhang; Dong-Jun Yu; Yang Zhang 040 (PLoS Comput. Biol., 2022)

MolMetaLM: a Physicochemical Knowledge-Guided Molecular Meta Language Model. - Yifan Wu; Min Zeng; Yang Li 107; Yang Zhang 040; Min Li (CoRR, 2024)

TM-search: An Efficient and Effective Tool for Protein Structure Database Search. - Zi Liu; Chengxin Zhang; Qidi Zhang; Yang Zhang 040; Dong-Jun Yu (J. Chem. Inf. Model., 2024)

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". - Ivona Martinovic; Tin Vlasic; Yang Li 107; Bryan Hooi; Yang Zhang 040; Mile Sikic (Zenodo, 2024)

Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction". - Ivona Martinovic; Tin Vlasic; Yang Li 107; Bryan Hooi; Yang Zhang 040; Mile Sikic (Zenodo, 2024)