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Author Details

Jeffrey J Gray
Johns Hopkins University
2000
140
47
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36111441De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD).Proteins2023
36111441De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD).Proteins2023
37701412Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032].Heliyon2023
37409346Structure-based neural network protein-carbohydrate interaction predictions at the residue level.Front Bioinform2023
37311043Fate and Efficacy of Engineered Allogeneic Stem Cells Targeting Cell Death and Proliferation Pathways in Primary and Brain Metastatic Lung Cancer.Stem Cells Transl Med2023
37185622Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies.Nat Commun2023
36993750Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level.bioRxiv2023
36683173Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features.MAbs2023
37425950Implicit model to capture electrostatic features of membrane environment.bioRxiv2023
37425754Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.bioRxiv2023
37503113Contextual protein and antibody encodings from equivariant graph transformers.bioRxiv2023
37484815AI Models for Protein Design are Driving Antibody Engineering.Curr Opin Biomed Eng2023
37546760Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange.bioRxiv2023
37035348Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.Heliyon2023
37484815AI Models for Protein Design are Driving Antibody Engineering.Curr Opin Biomed Eng2023
37701412Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032].Heliyon2023
37546760Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange.bioRxiv2023
37503113Contextual protein and antibody encodings from equivariant graph transformers.bioRxiv2023
37425950Implicit model to capture electrostatic features of membrane environment.bioRxiv2023
36993750Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level.bioRxiv2023
37425754Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.bioRxiv2023
37185622Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies.Nat Commun2023
37409346Structure-based neural network protein-carbohydrate interaction predictions at the residue level.Front Bioinform2023
37311043Fate and Efficacy of Engineered Allogeneic Stem Cells Targeting Cell Death and Proliferation Pathways in Primary and Brain Metastatic Lung Cancer.Stem Cells Transl Med2023
37035348Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.Heliyon2023
36683173Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features.MAbs2023
34978923"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19.CBE Life Sci Educ2022
35658008Induced fit with replica exchange improves protein complex structure prediction.PLoS Comput Biol2022
35704640Simultaneous prediction of antibody backbone and side-chain conformations with deep learning.PLoS One2022
36341416Hallucinating structure-conditioned antibody libraries for target-specific binders.Front Immunol2022
35871543Affinity maturation of TCR-like antibodies using phage display guided by structural modeling.Protein Eng Des Sel2022
35667008Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design".J Chem Theory Comput2022
35254891Accurate positioning of functional residues with robotics-inspired computational protein design.Proc Natl Acad Sci U S A2022
34978923"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19.CBE Life Sci Educ2022
35704640Simultaneous prediction of antibody backbone and side-chain conformations with deep learning.PLoS One2022
35667008Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design".J Chem Theory Comput2022
35658008Induced fit with replica exchange improves protein complex structure prediction.PLoS Comput Biol2022
36341416Hallucinating structure-conditioned antibody libraries for target-specific binders.Front Immunol2022
35871543Affinity maturation of TCR-like antibodies using phage display guided by structural modeling.Protein Eng Des Sel2022
35254891Accurate positioning of functional residues with robotics-inspired computational protein design.Proc Natl Acad Sci U S A2022
33360497Advances to tackle backbone flexibility in protein docking.Curr Opin Struct Biol2021
33539768An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.Structure2021
33764990Robustification of RosettaAntibody and Rosetta SnugDock.PLoS One2021
34322281Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.ACS Catal2021
34310137Diverse Scientific Benchmarks for Implicit Membrane Energy Functions.J Chem Theory Comput2021
34302669Membrane Protein Engineering with Rosetta.Methods Mol Biol2021
34133179Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta.J Phys Chem B2021
33360497Advances to tackle backbone flexibility in protein docking.Curr Opin Struct Biol2021
34625746The structural basis of PTEN regulation by multi-site phosphorylation.Nat Struct Mol Biol2021
34551980Shotgun scanning glycomutagenesis: A simple and efficient strategy for constructing and characterizing neoglycoproteins.Proc Natl Acad Sci U S A2021
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Collaborators

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Co-authored papers 18
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Co-authored papers 13
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Co-authored papers 11
Michael S Pacella
Co-authored papers 11
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University of Washington
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Chaok Seok
Seoul National University
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Alexandre M J J Bonvin
Bijvoet Center for Biomolecular Research, Utrecht University
Co-authored papers 4
Frank DiMaio
University of Washington
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Sheng-You Huang
Huazhong University of Science and Technology
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Huan-Xiang Zhou
University of Illinois Chicago
Co-authored papers 4
Rocco Moretti
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Xiaoqin Zou
Dalton Cardiovascular Research Center, University of Missouri
Co-authored papers 4
Ron Jacak
Co-authored papers 4
Panagiotis L Kastritis
Interdisciplinary Research Center HALOmem, Martin Luther University Halle-Wittenberg
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