Skip to Main Content

Author Details

Chengxin Zhang
University of Michigan ann arbor
2017
53
21
PMIDPaper TitleJournal TitlePublished Year
37522378BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic Acids Res2024
38014200Remodelling of Skeletal Muscle Myosin Metabolic States in Hibernating Mammals.bioRxiv2024
36524855From Protein Sequence to Structure: The Next Frontier in Cross-Species Extrapolation for Chemical Safety Evaluations.Environ Toxicol Chem2023
38013998A large-scale assessment of sequence database search tools for homology-based protein function prediction.bioRxiv2023
37479079Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models.J Mol Biol2023
37010520PDC: a highly compact file format to store protein 3D coordinates.Database (Oxford)2023
37340457BeEM: fast and faithful conversion of mmCIF format structure files to PDB format.BMC Bioinformatics2023
37356900rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.J Mol Biol2023
34375400EDIL3 deficiency ameliorates adverse cardiac remodelling by neutrophil extracellular traps (NET)-mediated macrophage polarization.Cardiovasc Res2022
35844960Progressive assembly of multi-domain protein structures from cryo-EM density maps.Nat Comput Sci2022
35439173Soluble CD13 induces inflammatory arthritis by activating the bradykinin receptor B1.J Clin Invest2022
35788567Generation of a live attenuated influenza A vaccine by proteolysis targeting.Nat Biotechnol2022
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
35362469CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures.Acta Crystallogr D Struct Biol2022
35561202AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.Bioinformatics2022
36548439Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.PLoS Comput Biol2022
36248743A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs.iScience2022
36038728US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nat Methods2022
35931779I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nat Protoc2022
34978562GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool.Bioinformatics2022
35247097RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control.Cell Mol Life Sci2022
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
33770072Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.PLoS Comput Biol2021
33741411Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli.J Mol Biol2021
33539887ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities.J Mol Biol2021
33803409Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis.Int J Mol Sci2021
34382712Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14.Proteins2021
34408149Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions.Nat Commun2021
34346740hiPSC Modeling of Lineage-Specific Smooth Muscle Cell Defects Caused by <i>TGFBR1</i><sup><i>A230T</i></sup> Variant, and Its Therapeutic Implications for Loeys-Dietz Syndrome.Circulation2021
34331351Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14.Proteins2021
34355210Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations.Cell Rep Methods2021
32511314Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1.bioRxiv2020
33083802Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps.bioRxiv2020
33175551Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2.J Proteome Res2020
32935105Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2.bioRxiv2020
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
31161212RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.Bioinformatics2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31581775Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge.J Proteome Res2019
31407406Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13.Proteins2019
31459527Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion.ACS Omega2019
31427836I-TASSER gateway: A protein structure and function prediction server powered by XSEDE.Future Gener Comput Syst2019
31341084Assembling multidomain protein structures through analogous global structural alignments.Proc Natl Acad Sci U S A2019
31070716ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.Bioinformatics2019
31081035LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.Nucleic Acids Res2019
29082551Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.Proteins2018
30265558Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17.J Proteome Res2018
29534977MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.J Mol Biol2018
27899282BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts.J Mol Biol2017
  • 1 - 50 of 53

Recommended Authors

Neeladri Sen
Institute of Structural and Molecular Biology, University College London
Career Start Year 2017
Number of shared co-authors 5
Tsukasa Nakamura
Purdue University
Career Start Year 2016
Number of shared co-authors 4
Minkyung Baek
Seoul National University
Career Start Year 2016
Number of shared co-authors 5
Mihaly Varadi
European Bioinformatics Institute
Career Start Year 2014
Number of shared co-authors 6
Chengfei Yan
Huazhong University of Science and Technology
Career Start Year 2013
Number of shared co-authors 4
Jian Peng
University of Illinois
Career Start Year 2009
Number of shared co-authors 0
Joan Segura
University of California San Diego
Career Start Year 2009
Number of shared co-authors 4
Zheng Wang
University of Miami
Career Start Year 2009
Number of shared co-authors 71
Sheng Wang
University of Texas at Arlington
Career Start Year 2008
Number of shared co-authors 0
Xin Gao
King Abdullah University of Science and Technology (KAUST)
Career Start Year 2007
Number of shared co-authors 4
Jiangning Song
Monash Data Futures Institute, Monash University
Career Start Year 2004
Number of shared co-authors 1
Jinbo Xu
Toyota Technological Institute at Chicago
Career Start Year 2003
Number of shared co-authors 1
Dmitry Korkin
Worcester Polytechnic Institute
Career Start Year 2002
Number of shared co-authors 1
Narcis Fernandez-Fuentes
Institute of Biological, Aberystwyth University
Career Start Year 2002
Number of shared co-authors 5
Jo??o P G L M Rodrigues
Stanford University
Career Start Year 1999
Number of shared co-authors 5
Jun-Tao Guo
University of North Carolina at Charlotte
Career Start Year 1999
Number of shared co-authors 0
Marc A Marti-Renom
Universitat Pompeu Fabra (UPF)
Career Start Year 1998
Number of shared co-authors 3
Dong Xu
University of Missouri
Career Start Year 1998
Number of shared co-authors 6
Daron M Standley
Osaka university
Career Start Year 1998
Number of shared co-authors 6
Chaok Seok
Seoul National University
Career Start Year 1998
Number of shared co-authors 12
Kentaro Tomii
National Institute of Advanced Industrial Science and Technology (AIST)
Career Start Year 1996
Number of shared co-authors 4
Lukasz Jaroszewski
University of California Riverside School of Medicine
Career Start Year 1995
Number of shared co-authors 4
Bonnie Berger
Massachusetts Institute of Technology
Career Start Year 1994
Number of shared co-authors 4
Jaap Heringa
VU University Amsterdam
Career Start Year 1991
Number of shared co-authors 0
Ram Samudrala
Jacobs School of Medicine and Biomedical Sciences, University at Buffalo
Career Start Year 1990
Number of shared co-authors 0
Roland L Dunbrack
Fox Chase Cancer Center
Career Start Year 1989
Number of shared co-authors 18
Ramanathan Sowdhamini
Indian Institute of Science
Career Start Year 1989
Number of shared co-authors 3
Adam Godzik
University of California Riverside
Career Start Year 1987
Number of shared co-authors 13
Andrej Sali (CM4AI)
University of California San Francisco
Career Start Year 1985
Number of shared co-authors 11
Andras Fiser
Albert Einstein College of Medicine
Career Start Year 1968
Number of shared co-authors 3

Collaborators

Yang Zhang
University of Michigan ann arbor
Co-authored papers 25
Wei Zheng
University of Michigan ann arbor
Co-authored papers 15
Peter L Freddolino
University of Michigan ann arbor
Co-authored papers 7
Anna Marie Pyle
Yale University, USA Howard Hughes Medical Institute
Co-authored papers 7
Gilbert S Omenn
and School of Public Health, University of Michigan ann arbor
Co-authored papers 6
Naihui Zhou
The First Affiliated Hospital of Soochow University
Co-authored papers 1
Maria J Martin
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 1
Md Nafiz Hamid
Iowa State University
Co-authored papers 1
Larry Davis
Co-authored papers 1
Radoslav Davidovic
Institute of Nuclear Sciences Vinca, University of Belgrade
Co-authored papers 1
Mohammad R K Mofrad
University of California Berkeley
Co-authored papers 1
Sa??o D??eroski
Jozef Stefan Institute
Co-authored papers 1
Domenico Cozzetto
Imperial College London
Co-authored papers 1
Marco Mesiti
Universita degli Studi di Milano
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
Rui Fa
University College London
Co-authored papers 1
Sabeur Aridhi
Universite de Lorraine, CNRS
Co-authored papers 1
Qizhong Mao
Temple University
Co-authored papers 1
Fabio Fabris
University of Kent
Co-authored papers 1
Wei-Cheng Tseng
Taipei Veterans General Hospital
Co-authored papers 1
Christophe Dessimoz
University of Lausanne
Co-authored papers 1
Gage S Black
Brigham Young University
Co-authored papers 1
Suyang Dai
Fudan University
Co-authored papers 1
Maxat Kulmanov
King Abdullah University of Science and Technology.
Co-authored papers 1
Kai Hakala
University of Turku
Co-authored papers 1
Tomislav ??muc
Ruder Boskovic Institute
Co-authored papers 1
Giuseppe Profiti
University of Bologna
Co-authored papers 1
Olivier Lichtarge
Baylor College of Medicine
Co-authored papers 1
Release 1.2