Yang Zhang
Orcid: 0000-0002-2739-1916Affiliations:
- University of Michigan, Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
According to our database1,
Yang Zhang
authored at least 72 papers
between 2004 and 2024.
Collaborative distances:
Collaborative distances:
Timeline
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on orcid.org
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Bibliography
2024
J. Chem. Inf. Model., 2024
2022
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.
PLoS Comput. Biol., December, 2022
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.
Genom. Proteom. Bioinform., October, 2022
Fast and accurate Ab Initio Protein structure prediction using deep learning potentials.
PLoS Comput. Biol., September, 2022
Nat. Comput. Sci., 2022
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction.
Nucleic Acids Res., 2022
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation.
Nucleic Acids Res., 2022
Bioinform., 2022
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.
Briefings Bioinform., 2022
2021
Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders.
PLoS Comput. Biol., 2021
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.
PLoS Comput. Biol., 2021
MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction.
Bioinform., 2021
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.
Briefings Bioinform., 2021
2020
Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction.
IEEE Trans. Evol. Comput., 2020
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.
J. Chem. Inf. Model., 2020
J. Cheminformatics, 2020
FUpred: detecting protein domains through deep-learning-based contact map prediction.
Bioinform., 2020
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins.
Bioinform., 2020
Bioinform., 2020
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.
Bioinform., 2020
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.
Bioinform., 2020
CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm.
Bioinform., 2020
SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function.
Bioinform., 2020
Bioinform., 2020
Bioinform., 2020
2019
Detecting distant-homology protein structures by aligning deep neural-network based contact maps.
PLoS Comput. Biol., 2019
LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.
Nucleic Acids Res., 2019
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism.
J. Cheminformatics, 2019
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.
Future Gener. Comput. Syst., 2019
Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors.
Bioinform., 2019
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.
Bioinform., 2019
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.
Bioinform., 2019
2018
A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking.
Nucleic Acids Res., 2018
mTM-align: a server for fast protein structure database search and multiple protein structure alignment.
Nucleic Acids Res., 2018
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons.
J. Chem. Inf. Model., 2018
WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest.
Bioinform., 2018
LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.
Bioinform., 2018
Bioinform., 2018
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes.
Database J. Biol. Databases Curation, 2018
2017
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information.
Nucleic Acids Res., 2017
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly.
Nucleic Acids Res., 2017
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation.
Nucleic Acids Res., 2017
NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers.
Bioinform., 2017
2016
STRUM: structure-based prediction of protein stability changes upon single-point mutation.
Bioinform., 2016
Recognizing metal and acid radical ion-binding sites by integrating <i>ab initio</i> modeling with template-based transferals.
Bioinform., 2016
Bioinform., 2016
2015
Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles.
PLoS Comput. Biol., 2015
Nucleic Acids Res., 2015
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces.
BMC Bioinform., 2015
Accurate disulfide-bonding network predictions improve <i>ab initio</i> structure prediction of cysteine-rich proteins.
Bioinform., 2015
Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning.
Bioinform., 2015
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations.
Bioinform., 2015
2013
An Evolution-Based Approach to <i>De Novo</i> Protein Design and Case Study on <i>Mycobacterium tuberculosis</i>.
PLoS Comput. Biol., 2013
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.
Nucleic Acids Res., 2013
EvoDesign: <i>de novo</i> protein design based on structural and evolutionary profiles.
Nucleic Acids Res., 2013
J. Chem. Inf. Model., 2013
Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition.
J. Comput. Biol., 2013
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment.
Bioinform., 2013
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling.
Bioinform., 2013
ThreaDom: extracting protein domain boundary information from multiple threading alignments.
Bioinform., 2013
An image-based multi-label human protein subcellular localization predictor (<i>i</i>Locator) reveals protein mislocalizations in cancer tissues.
Bioinform., 2013
Proceedings of the Research in Computational Molecular Biology, 2013
2012
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.
Nucleic Acids Res., 2012
2010
GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation.
Bioinform., 2010
Bioinform., 2010
2008
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction.
Bioinform., 2008
2006
Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
PLoS Comput. Biol., 2006
Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
PLoS Comput. Biol., 2006
2004
J. Comput. Chem., 2004
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
Bioinform., 2004