Yang Zhang

发表

Improving accuracy of protein contact prediction using balanced network deconvolution

Hong-Bin Shen, Hai-Ping Sun, Yan Huang, 2015, Proteins.

SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function

Yang Zhang, Xiaoqiang Huang, Wei Zheng, 2019, Bioinform..

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

Qi Wu, Yang Zhang, Jianyi Yang, 2018, Nucleic Acids Res..

Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli

Yang Zhang, Weikang Gong, Aysam Guerler, 2020, bioRxiv.

A Protocol for Computer-Based Protein Structure and Function Prediction

Dong Xu, Yang Zhang, Ambrish Roy, 2011, Journal of visualized experiments : JoVE.

TOUCHSTONE: A unified approach to protein structure prediction

Daisuke Kihara, Yang Zhang, Andrzej Kolinski, 2003, Proteins.

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction

Yang Zhang, Zhiping Weng, Thom Vreven, 2019, Bioinform..

Computational protein design and large-scale assessment by I-TASSER structure assembly simulations.

Yang Zhang, Andrea Bazzoli, Andrea G B Tettamanzi, 2011, Journal of molecular biology.

Search for β2 Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations

Yang Zhang, Qifeng Bai, Xiaojun Yao, 2014, PloS one.

I‐TASSER: Fully automated protein structure prediction in CASP8

Yang Zhang, Yang Zhang, 2009, Proteins.

Identification of near‐native structures by clustering protein docking conformations

Yang Zhang, Stephan Lorenzen, Yang Zhang, 2007, Proteins.

MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.

Yang Zhang, Jouko J Virtanen, Yang Zhang, 2018, Acta crystallographica. Section D, Structural biology.

A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.

Hong-Bin Shen, Yang Zhang, Biao Zhang, 2020, Journal of molecular biology.

Text Mining for Bioinformatics: State of the Art Review

Yang Zhang, Min Song, Yanliang Qi, 2009, 2009 2nd IEEE International Conference on Computer Science and Information Technology.

Template‐based protein structure prediction in CASP11 and retrospect of I‐TASSER in the last decade

Hong-Bin Shen, Yang Zhang, Jianyi Yang, 2016, Proteins.

Ensembling multiple raw coevolutionary features with deep residual neural networks for contact‐map prediction in CASP13

Yang Zhang, Yang Li, Dong-Jun Yu, 2019, Proteins.

ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons

Jun Hu, Yang Zhang, Yang Li, 2018, J. Chem. Inf. Model..

Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors

Yang Zhang, Xiaoyan Ke, Tao Pang, 2019, Bioinform..

A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data

Yong Qi, Yang Zhang, Dong-Jun Yu, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons

Zhiyong Lu, Yang Zhang, Peter L. Freddolino, 2020, Bioinform..

mTM-align: a server for fast protein structure database search and multiple protein structure alignment

Yang Zhang, Jianyi Yang, Zhenling Peng, 2018, Nucleic Acids Res..

Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

Yang Zhang, Chengxin Zhang, Baoji He, 2018, Proteins.

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins

Yang Zhang, Wei Zheng, Yang Li, 2019, Bioinform..

FASPR: an open-source tool for fast and accurate protein side-chain packing

Yang Zhang, Xiaoqiang Huang, Robin Pearce, 2020, Bioinform..

Detecting distant-homology protein structures by aligning deep neural-network based contact maps

Yang Zhang, Wei Zheng, Robin Pearce, 2019, PLoS Comput. Biol..

Deep‐learning contact‐map guided protein structure prediction in CASP13

Yang Zhang, Wei Zheng, Yang Li, 2019, Proteins.

FUpred: detecting protein domains through deep-learning-based contact map prediction

Xiaogen Zhou, Yang Zhang, Wei Zheng, 2020, Bioinform..

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Yang Zhang, Peter L. Freddolino, Wei Zheng, 2018, Journal of molecular biology.

Assembling multidomain protein structures through analogous global structural alignments

Xiaogen Zhou, Yang Zhang, Jun Hu, 2019, Proceedings of the National Academy of Sciences.

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

Xiaogen Zhou, Yang Zhang, Chengxin Zhang, 2020, bioRxiv.

CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm

Yang Zhang, Jun Liu, Gui-Jun Zhang, 2019, Bioinform..

EvoEF2: accurate and fast energy function for computational protein design

Yang Zhang, Xiaoqiang Huang, Robin Pearce, 2019, Bioinform..

ResQ: An Approach to Unified Estimation of B-Factor and Residue-Specific Error in Protein Structure Prediction.

Yan Wang, Yang Zhang, Jianyi Yang, 2016, Journal of molecular biology.

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism

Yang Zhang, Eric W. Bell, Eric W Bell, 2019, Journal of Cheminformatics.

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

Yang Zhang, Jian Zhang, Yang Zhang, 2010, PloS one.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

Template‐based modeling and free modeling by I‐TASSER in CASP7

Yang Zhang, Yang Zhang, 2007, Proteins.