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Author Details

Yang Zhang
University of Michigan ann arbor
2002
183
59
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37522378BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic Acids Res2024
37522378BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic Acids Res2024
36524855From Protein Sequence to Structure: The Next Frontier in Cross-Species Extrapolation for Chemical Safety Evaluations.Environ Toxicol Chem2023
36656852De novo protein fold design through sequence-independent fragment assembly simulations.Proc Natl Acad Sci U S A2023
36828268ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.J Mol Biol2023
37356900rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.J Mol Biol2023
36851671Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals.Viruses2023
36524855From Protein Sequence to Structure: The Next Frontier in Cross-Species Extrapolation for Chemical Safety Evaluations.Environ Toxicol Chem2023
37356900rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.J Mol Biol2023
36656852De novo protein fold design through sequence-independent fragment assembly simulations.Proc Natl Acad Sci U S A2023
36851671Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals.Viruses2023
36828268ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.J Mol Biol2023
34800783The molecular mechanisms of ferroptosis and its role in cardiovascular disease.Biomed Pharmacother2022
36038728US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nat Methods2022
35568117TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.Genomics Proteomics Bioinformatics2022
35663033Deep learning geometrical potential for high-accuracy <i>ab initio</i> protein structure prediction.iScience2022
36548439Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.PLoS Comput Biol2022
34800783The molecular mechanisms of ferroptosis and its role in cardiovascular disease.Biomed Pharmacother2022
35247097RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control.Cell Mol Life Sci2022
35663033Deep learning geometrical potential for high-accuracy <i>ab initio</i> protein structure prediction.iScience2022
35568117TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.Genomics Proteomics Bioinformatics2022
36548439Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.PLoS Comput Biol2022
36038728US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nat Methods2022
35247097RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control.Cell Mol Life Sci2022
32436937Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.Brief Bioinform2021
32436937Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.Brief Bioinform2021
33591954Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function.J Clin Invest2021
33741411Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli.J Mol Biol2021
34204123The Fungal Effector Mlp37347 Alters Plasmodesmata Fluxes and Enhances Susceptibility to Pathogen.Microorganisms2021
34196616Crystal and solution structures of a novel antimicrobial peptide from Chrysomya megacephala.Acta Crystallogr D Struct Biol2021
33441130Elevated lymphotoxin-α (TNFβ) is associated with intervertebral disc degeneration.BMC Musculoskelet Disord2021
33397114Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations.J Phys Chem B2021
33393786Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.J Proteome Res2021
34529671Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders.PLoS Comput Biol2021
33741411Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli.J Mol Biol2021
33591954Endoplasmic reticulum-associated degradation is required for nephrin maturation and kidney glomerular filtration function.J Clin Invest2021
34529671Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders.PLoS Comput Biol2021
34204123The Fungal Effector Mlp37347 Alters Plasmodesmata Fluxes and Enhances Susceptibility to Pathogen.Microorganisms2021
34196616Crystal and solution structures of a novel antimicrobial peptide from Chrysomya megacephala.Acta Crystallogr D Struct Biol2021
33397114Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations.J Phys Chem B2021
33393786Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.J Proteome Res2021
33441130Elevated lymphotoxin-α (TNFβ) is associated with intervertebral disc degeneration.BMC Musculoskelet Disord2021
31274151Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.Bioinformatics2020
32200634Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1.J Proteome Res2020
31851497Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.J Chem Inf Model2020
32259206FASPR: an open-source tool for fast and accurate protein side-chain packing.Bioinformatics2020
31637787Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation.Mol Microbiol2020
31588495EvoEF2: accurate and fast energy function for computational protein design.Bioinformatics2020
31830252SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function.Bioinformatics2020
32544884<i>De novo</i> design of protein peptides to block association of the SARS-CoV-2 spike protein with human ACE2.Aging (Albany NY)2020
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Collaborators

Chengxin Zhang
University of Michigan ann arbor
Co-authored papers 25
Dong Xu
University of Missouri
Co-authored papers 14
Gilbert S Omenn
and School of Public Health, University of Michigan ann arbor
Co-authored papers 13
Wei Zheng
University of Michigan ann arbor
Co-authored papers 10
Rajasree Menon
University of Michigan Medical School ann arbor
Co-authored papers 7
Peter L Freddolino
University of Michigan ann arbor
Co-authored papers 6
Daisuke Kihara
Purdue University
Co-authored papers 6
Yuanfang Guan
University of Michigan ann arbor
Co-authored papers 3
Torsten Schwede
University of Basel
Co-authored papers 2
Christine Orengo
University College London, Institute of Structural and Molecular Biology
Co-authored papers 2
Peter W Rose
University of California
Co-authored papers 2
Jianlin Cheng
University of Missouri
Co-authored papers 2
Kevin P Battaile
Co-authored papers 2
Lydie Lane
SIB Swiss Institute of Bioinformatics and University of Geneva
Co-authored papers 2
Sean D Mooney
University of Washington
Co-authored papers 2
Ian Sillitoe
University College London
Co-authored papers 2
Jie Hou
Saint Louis University
Co-authored papers 2
Anna Marie Pyle
Yale University, USA Howard Hughes Medical Institute
Co-authored papers 2
David Baker
University of Washington
Co-authored papers 2
Liam J McGuffin
University of Reading
Co-authored papers 2
Renzhi Cao
Pacific Lutheran University
Co-authored papers 2
Timothy Bergquist
University of Washington School of Medicine
Co-authored papers 2
Stephen K Burley
The State University of New Jersey
Co-authored papers 2
Christoph H Borchers
McGill University
Co-authored papers 2
Ariel Rokem
University of Washington, Department of Psychology and eScience Institute
Co-authored papers 1
Marco Mesiti
Universita degli Studi di Milano
Co-authored papers 1
Arzucan ÿzgür
Co-authored papers 1
Neven Sumonja
Institute of Nuclear Sciences VINCA, University of Belgrade
Co-authored papers 1
Magdalena Kotlicka-Antczak
Medical University of Lodz
Co-authored papers 1
Alan J Medlar
Co-authored papers 1
Release 1.2