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Author Details

David E Shaw
Columbia University
2000
138
73
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36524993Gating and modulation of an inward-rectifier potassium channel.J Gen Physiol2023
37059095Desensitization dynamics of the AMPA receptor.Structure2023
37086179Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography.J Chem Inf Model2023
37019905Structural mechanism of a drug-binding process involving a large conformational change of the protein target.Nat Commun2023
37378552A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis.J Chem Inf Model2023
37270847RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across FGFR2 Alterations and Resistance Mutations.Cancer Discov2023
35260847Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.Nat Struct Mol Biol2022
35694853Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.J Phys Chem B2022
35130691Molecular Basis of Small-Molecule Binding to α-Synuclein.J Am Chem Soc2022
35239648How does a small molecule bind at a cryptic binding site?PLoS Comput Biol2022
35108525Targetable HER3 functions driving tumorigenic signaling in HER2-amplified cancers.Cell Rep2022
34625747A structural model of a Ras-Raf signalosome.Nat Struct Mol Biol2021
33883267Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.Proc Natl Acad Sci U S A2021
33568655Quantum chemical benchmark databases of gold-standard dimer interaction energies.Sci Data2021
33568355Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling.Cancer Discov2021
33758867Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.bioRxiv2021
33891001Suppressing Kv1.3 Ion Channel Activity with a Novel Small Molecule Inhibitor Ameliorates Inflammation in a Humanised Mouse Model of Ulcerative Colitis.J Crohns Colitis2021
34400635Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization.Nat Commun2021
32323533Mechanism of Coupled Folding-upon-Binding of an Intrinsically Disordered Protein.J Am Chem Soc2020
31914313Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes.J Chem Theory Comput2020
33317288Midtown splines: An optimal charge assignment for electrostatics calculations.J Chem Phys2020
32639159AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets.J Chem Inf Model2020
32672461Structural Basis of AZD9291 Selectivity for EGFR T790M.J Med Chem2020
32697578A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery.J Chem Inf Model2020
30504785Publisher Correction: Structural insights into binding specificity, efficacy and bias of a β<sub>2</sub>AR partial agonist.Nat Chem Biol2019
30760596Atomic-level characterization of protein-protein association.Proc Natl Acad Sci U S A2019
30875465Fragment Hits: What do They Look Like and How do They Bind?J Med Chem2019
31019091Structural mechanism for Bruton's tyrosine kinase activation at the cell membrane.Proc Natl Acad Sci U S A2019
29735687Developing a molecular dynamics force field for both folded and disordered protein states.Proc Natl Acad Sci U S A2018
30102523Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule.Biochemistry2018
30337523The architecture of EGFR's basal complexes reveals autoinhibition mechanisms in dimers and oligomers.Nat Commun2018
30277396Atomic-Level Description of Protein Folding inside the GroEL Cavity.J Phys Chem B2018
30327561Structural insights into binding specificity, efficacy and bias of a β<sub>2</sub>AR partial agonist.Nat Chem Biol2018
29670280Mechanism of NMDA receptor channel block by MK-801 and memantine.Nature2018
29378935RNA force field with accuracy comparable to state-of-the-art protein force fields.Proc Natl Acad Sci U S A2018
28760994Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS).Proc Natl Acad Sci U S A2017
29096510Improving the accuracy of Møller-Plesset perturbation theory with neural networks.J Chem Phys2017
28582625Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations.J Chem Theory Comput2017
26866996Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.J Chem Theory Comput2016
26266489Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.Protein Sci2016
27796308EGFR oligomerization organizes kinase-active dimers into competent signalling platforms.Nat Commun2016
26745425A Simple Model of Multivalent Adhesion and Its Application to Influenza Infection.Biophys J2016
26873858Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor.Mol Pharmacol2016
27082121Picosecond to Millisecond Structural Dynamics in Human Ubiquitin.J Phys Chem B2016
25524709Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage.Proteins2015
26305940Allosteric activation of apicomplexan calcium-dependent protein kinases.Proc Natl Acad Sci U S A2015
26404828Structural origin of slow diffusion in protein folding.Science2015
26089515SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins.Science2015
25924808Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations.J Am Chem Soc2015
26025225Identifying localized changes in large systems: Change-point detection for biomolecular simulations.Proc Natl Acad Sci U S A2015
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Collaborators

John Kuriyan
University of California berkeley
Co-authored papers 6
Natalia Jura
Cardiovascular Research Institute, University of California San Francisco
Co-authored papers 4
Aashish Manglik
Department of Pharmaceutical Chemistry, University of California San Francisco
Co-authored papers 3
Seth A Darst
The Rockefeller University
Co-authored papers 3
Michel Bouvier
Institute for Research in Immunology and Cancer, Universite de Montreal
Co-authored papers 2
Jo??o P G L M Rodrigues
Stanford University
Co-authored papers 2
Barton F Haynes
Co-authored papers 2
Paul Dominic B Olinares
The Rockefeller University
Co-authored papers 2
Robert Landick
University of Wisconsin-Madison
Co-authored papers 2
Brian T Chait
The Rockefeller University
Co-authored papers 2
Willy Wriggers
Old Dominion University
Co-authored papers 2
Shaun R Coughlin
Co-authored papers 2
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 1
David A Case
Rutgers University
Co-authored papers 1
Oliver F Lange
Center for Integrated Protein Science, Technische Universitat Munchen
Co-authored papers 1
Gordon C K Roberts
Leicester Institute of Structural and Chemical Biology, University of Leicester
Co-authored papers 1
Josep Rizo
University of Texas Southwestern Medical Center
Co-authored papers 1
Mike P Williamson
The University of Sheffield
Co-authored papers 1
Pasi A J??nne
Dana-Farber Cancer Institute
Co-authored papers 1
Lu-Yun Lian
Institute of Systems, The University of Liverpool
Co-authored papers 1
Hae Kyung Im
Co-authored papers 1
Igor L Barsukov
Institute of Integrative Biology, University of Liverpool
Co-authored papers 1
Ad Bax
National Institutes of Health
Co-authored papers 1
Patrick C A van der Wel
Zernike Institute for Advanced Materials, University of Groningen
Co-authored papers 1
David Middleton
Co-authored papers 1
Ioannis Vakonakis
University of Oxford
Co-authored papers 1
Kenneth D Westover
University of Texas Southwestern Medical Center
Co-authored papers 1
Jennifer E Kung
Cardiovascular Research Institute, University of California San Francisco
Co-authored papers 1
Thomas A Frenkiel
The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute
Co-authored papers 1
Thanh D Do
Co-authored papers 1
Release 1.2