Yang Zhang - RankMe

73 papers B 1Journal 72

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	MolMetaLM: a Physicochemical Knowledge-Guided Molecular Meta Language Model. CoRR Yifan Wu, Min Zeng, Yang Li, Yang Zhang, Min Li
2024	J	`jnl`	TM-search: An Efficient and Effective Tool for Protein Structure Database Search. J. Chem. Inf. Model. Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
2022	J	`jnl`	Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning. Briefings Bioinform. Biao Zhang, Dong Liu, Yang Zhang, Hong-Bin Shen, Gui-Jun Zhang
2022	J	`jnl`	DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Res. Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang
2022	J	`jnl`	Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. PLoS Comput. Biol. Robin Pearce, Yang Li, Gilbert S. Omenn, Yang Zhang
2022	J	`jnl`	GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. Bioinform. Elijah A. MacCarthy, Chengxin Zhang, Yang Zhang, Dukka B. KC
2022	J	`jnl`	Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS Comput. Biol. Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
2022	J	`jnl`	LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Res. Wei Zheng, Qiqige Wuyun, Xiaogen Zhou, Yang Li, P. L. Freddolino, Yang Zhang
2022	J	`jnl`	Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nat. Comput. Sci. Xiaogen Zhou, Yang Li, Chengxin Zhang, Wei Zheng, Guijun Zhang, Yang Zhang
2022	J	`jnl`	TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. Genom. Proteom. Bioinform. Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert S. Omenn, P. L. Freddolino, Dong-Jun Yu, Yang Zhang
2021	J	`jnl`	Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings Bioinform. Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
2021	J	`jnl`	Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS Comput. Biol. Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu, Yang Zhang
2021	J	`jnl`	MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinform. Kai-Long Zhao, Jun Liu, Xiao-Gen Zhou, Jianzhong Su, Yang Zhang, Gui-Jun Zhang
2021	J	`jnl`	Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PLoS Comput. Biol. Jaie C. Woodard, Wei Zheng, Yang Zhang
2020	J	`jnl`	Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinform. Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang, Yan Huang, Yang Zhang, Hong-Bin Shen
2020	J	`jnl`	CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinform. Jun Liu, Xiao-Gen Zhou, Yang Zhang, Gui-Jun Zhang
2020	J	`jnl`	DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinform. Chengxin Zhang, Wei Zheng, S. M. Mortuza, Yang Li, Yang Zhang
2020	J	`jnl`	Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinform. Xiaoqiong Wei, Chengxin Zhang, P. L. Freddolino, Yang Zhang, Zhiyong Lu
2020	J	`jnl`	EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. J. Cheminformatics Wenyi Zhang, Eric W. Bell, Minghao Yin, Yang Zhang
2020	J	`jnl`	EvoEF2: accurate and fast energy function for computational protein design. Bioinform. Xiaoqiang Huang, Robin Pearce, Yang Zhang
2020	J	`jnl`	FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinform. Xiaoqiang Huang, Robin Pearce, Yang Zhang
2020	J	`jnl`	FUpred: detecting protein domains through deep-learning-based contact map prediction. Bioinform. Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang
2020	J	`jnl`	Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinform. Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng
2020	J	`jnl`	SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinform. Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang
2020	J	`jnl`	Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. J. Chem. Inf. Model. Xiaoqiang Huang, Robin Pearce, Yang Zhang
2020	J	`jnl`	Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction. IEEE Trans. Evol. Comput. Xiaogen Zhou, Chunxiang Peng, Jun Liu, Yang Zhang, Gui-Jun Zhang
2019	J	`jnl`	Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLoS Comput. Biol. Wei Zheng, Qiqige Wuyun, Yang Li, S. M. Mortuza, Chengxin Zhang, Robin Pearce, Jishou Ruan, Yang Zhang
2019	J	`jnl`	DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. J. Cheminformatics Eric W. Bell, Yang Zhang
2019	J	`jnl`	I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. Future Gener. Comput. Syst. Wei Zheng, Chengxin Zhang, Eric W. Bell, Yang Zhang
2019	J	`jnl`	LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Res. Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang
2019	J	`jnl`	Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors. Bioinform. Jiansheng Wu, Ben Liu, Wallace K. B. Chan, Weijian Wu, Tao Pang, Haifeng Hu, Shancheng Yan, Xiaoyan Ke, Yang Zhang
2019	J	`jnl`	RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinform. Sha Gong, Chengxin Zhang, Yang Zhang
2019	J	`jnl`	ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinform. Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
2018	J	`jnl`	A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. Chun-Qiu Xia, Ke Han, Yong Qi, Yang Zhang, Dong-Jun Yu
2018	J	`jnl`	ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. J. Chem. Inf. Model. Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu
2018	J	`jnl`	COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Res. Qi Wu, Zhenling Peng, Yang Zhang, Jianyi Yang
2018	J	`jnl`	LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinform. Jun Hu, Zi Liu, Dong-Jun Yu, Yang Zhang
2018	J	`jnl`	THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. Database J. Biol. Databases Curation Justin S. Diamond, Yang Zhang
2018	J	`jnl`	WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. Bioinform. Jiansheng Wu, Qiuming Zhang, Weijian Wu, Tao Pang, Haifeng Hu, Wallace K. B. Chan, Xiaoyan Ke, Yang Zhang
2018	J	`jnl`	mTM-align: a server for fast protein structure database search and multiple protein structure alignment. Nucleic Acids Res. Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang
2018	J	`jnl`	mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinform. Runze Dong, Zhenling Peng, Yang Zhang, Jianyi Yang
2017	J	`jnl`	COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Res. Chengxin Zhang, P. L. Freddolino, Yang Zhang
2017	J	`jnl`	I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. Nucleic Acids Res. Yan Wang, Jouko Virtanen, Zhidong Xue, Yang Zhang
2017	J	`jnl`	NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinform. Baoji He, S. M. Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang
2017	J	`jnl`	ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Res. Yan Wang, Jian Wang, Ruiming Li, Qiang Shi, Zhidong Xue, Yang Zhang
2016	J	`jnl`	3DRobot: automated generation of diverse and well-packed protein structure decoys. Bioinform. Haiyou Deng, Ya Jia, Yang Zhang
2016	J	`jnl`	Recognizing metal and acid radical ion-binding sites by integrating Bioinform. Xiuzhen Hu, Qiwen Dong, Jianyi Yang, Yang Zhang
2016	J	`jnl`	STRUM: structure-based prediction of protein stability changes upon single-point mutation. Bioinform. Lijun Quan, Qiang Lv, Yang Zhang
2015	J	`jnl`	Accurate disulfide-bonding network predictions improve Bioinform. Jing Yang, Bao-Ji He, Richard Jang, Yang Zhang, Hong-Bin Shen
2015	J	`jnl`	Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. Bioinform. Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen
2015	J	`jnl`	GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. Bioinform. Wallace K. B. Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey R. Brender, Junguk Hur, Arzucan Özgür, Yang Zhang
2015	J	`jnl`	I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res. Jianyi Yang, Yang Zhang
2015	J	`jnl`	PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. BMC Bioinform. Shanshan Cheng, Yang Zhang, Charles L. Brooks III
2015	J	`jnl`	Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. PLoS Comput. Biol. Jeffrey R. Brender, Yang Zhang
2013	J	`jnl`	An Evolution-Based Approach to PLoS Comput. Biol. Pralay Mitra, David Shultis, Jeffrey R. Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang
2013	J	`jnl`	An image-based multi-label human protein subcellular localization predictor ( Bioinform. Ying-Ying Xu, Fan Yang, Yang Zhang, Hong-Bin Shen
2013	J	`jnl`	BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res. Jianyi Yang, Ambrish Roy, Yang Zhang
2013	J	`jnl`	EvoDesign: Nucleic Acids Res. Pralay Mitra, David Shultis, Yang Zhang
2013	B	`conf`	Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. RECOMB Dong Xu, Hua Li, Yang Zhang
2013	J	`jnl`	High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. Bioinform. Jing Yang, Richard Jang, Yang Zhang, Hong-Bin Shen
2013	J	`jnl`	Mapping Monomeric Threading to Protein-Protein Structure Prediction. J. Chem. Inf. Model. Aysam Guerler, Brandon Govindarajoo, Yang Zhang
2013	J	`jnl`	Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition. J. Comput. Biol. Dong Xu, Hua Li, Yang Zhang
2013	J	`jnl`	Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinform. Jianyi Yang, Ambrish Roy, Yang Zhang
2013	J	`jnl`	ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinform. Zhidong Xue, Dong Xu, Yan Wang, Yang Zhang
2012	J	`jnl`	COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res. Ambrish Roy, Jianyi Yang, Yang Zhang
2010	J	`jnl`	GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation. Bioinform. Jian Zhang, Yang Zhang
2010	J	`jnl`	How significant is a protein structure similarity with TM-score = 0.5? Bioinform. Jinrui Xu, Yang Zhang
2008	J	`jnl`	A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinform. Sitao Wu, Yang Zhang
2008	J	`jnl`	I-TASSER server for protein 3D structure prediction. BMC Bioinform. Yang Zhang
2006	J	`jnl`	Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. PLoS Comput. Biol. Yang Zhang, Mark E. DeVries, Jeffrey Skolnick
2006	J	`jnl`	Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. PLoS Comput. Biol. Yang Zhang, Mark E. DeVries, Jeffrey Skolnick
2004	J	`jnl`	Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinform. Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick
2004	J	`jnl`	SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem. Yang Zhang, Jeffrey Skolnick