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Author Details

Henry van den Bedem
University of California San Francisco
2002
133
27
PMIDPaper TitleJournal TitlePublished Year
37425870Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM.bioRxiv2024
37143823Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.Front Mol Biosci2023
36993233Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors.bioRxiv2023
37408369SARS-CoV-2 main protease mutation analysis via a kinematic method.Proteins2023
35235748AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens.J Chem Inf Model2022
35594568Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease.J Chem Inf Model2022
35312477Ligand binding remodels protein side-chain conformational heterogeneity.Elife2022
33210433qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.Protein Sci2021
34258328Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.Struct Dyn2021
33301748Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion.Biophys J2021
32148858Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.IUCrJ2020
30894496Cryo-EM structures of <i>Helicobacter pylori</i> vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution.Proc Natl Acad Sci U S A2019
31721579Transport Properties of Nanoporous, Chemically Forced Biological Lattices.J Phys Chem B2019
31801874Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.Proc Natl Acad Sci U S A2019
31274417Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation.J Synchrotron Radiat2019
29315667Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces.J Comput Chem2018
30240209Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion.J Chem Inf Model2018
29899515Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins.ISME J2018
30297780Reply to 'Misreading chaperone-substrate complexes from random noise'.Nat Struct Mol Biol2018
30457858qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.J Med Chem2018
28009548Conformational variation of proteins at room temperature is not dominated by radiation damage.J Synchrotron Radiat2017
28334257Fast, clash-free RNA conformational morphing using molecular junctions.Bioinformatics2017
28677304Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.Environ Microbiol Rep2017
28597937Frustration-guided motion planning reveals conformational transitions in proteins.Proteins2017
26894537Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca(2+)-calmodulin.Acta Crystallogr D Struct Biol2016
27239796Visualizing chaperone-assisted protein folding.Nat Struct Mol Biol2016
27028235Probing RNA Native Conformational Ensembles with Structural Constraints.J Comput Biol2016
26756780Coupled Motions in β2AR:Gαs Conformational Ensembles.J Chem Theory Comput2016
25825836Integrative, dynamic structural biology at atomic resolution--it's about time.Nat Methods2015
26506617Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.PLoS Comput Biol2015
26422513Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.Elife2015
26636932Tau-ism: The Yin and Yang of Microtubule Sliding, Detachment, and Rupture.Biophys J2015
26213417Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations.J Mech Phys Solids2015
26218073Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.PLoS Comput Biol2015
24474795Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.Proc Natl Acad Sci U S A2014
25114056Characterizing RNA ensembles from NMR data with kinematic models.Nucleic Acids Res2014
24882744Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.Structure2014
23913260Automated identification of functional dynamic contact networks from X-ray crystallography.Nat Methods2013
21460455Distributed structure determination at the JCSG.Acta Crystallogr D Biol Crystallogr2011
21918110Accessing protein conformational ensembles using room-temperature X-ray crystallography.Proc Natl Acad Sci U S A2011
19913036Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.J Mol Biol2010
20836087The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu.Protein Sci2010
20944232Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944231Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944230Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944229Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944228The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944225Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944224Structure of Bacteroides thetaiotaomicron BT2081 at 2.05⿿ÿ resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
20944223A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2⿿ÿ resolution.Acta Crystallogr Sect F Struct Biol Cryst Commun2010
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Collaborators

Ashley M Deacon
Accelero Biostructures Inc., USA XPose Therapeutics Inc.
Co-authored papers 93
Mitchell D Miller
Rice University
Co-authored papers 90
Lukasz Jaroszewski
University of California Riverside School of Medicine
Co-authored papers 89
Adam Godzik
University of California Riverside
Co-authored papers 89
John Wooley
University of California
Co-authored papers 89
Keith O Hodgson
Stanford University
Co-authored papers 89
Scott A Lesley
Merck & Co., Inc.
Co-authored papers 89
Ian A Wilson
The Scripps Research Institute, USA The Skaggs Institute for Chemical Biology
Co-authored papers 89
Marc-Andr?? Elsliger
Joint Center for Structural Genomics
Co-authored papers 89
Heath E Klock
Merck & Co., Inc.
Co-authored papers 89
Daniel McMullan
Genomics Institute of the Novartis Research Foundation
Co-authored papers 86
Qingping Xu
Argonne National Laboratory
Co-authored papers 81
Andrew T Morse
Co-authored papers 78
Polat Abdubek
Regeneron Pharmaceuticals, Inc.
Co-authored papers 73
Hsiu-Ju Chiu
Joint Center for Structural Genomics
Co-authored papers 72
Slawomir K Grzechnik
Co-authored papers 71
Ron Reyes
Co-authored papers 67
Edward Nigoghossian
Genomics Institute of the Novartis Research Foundation
Co-authored papers 61
Gye Won Han
Bridge Institute, University of Southern California
Co-authored papers 58
Herbert L Axelrod
Joint Center for Structural Genomics
Co-authored papers 53
Sanjay Krishna
Institute of Science, Banaras Hindu University
Co-authored papers 52
Christopher L Rife
The Joint Center for Structural Genomics, Stanford University
Co-authored papers 49
Mark W Knuth
Joint Center for Structural Genomics
Co-authored papers 48
Peter Kuhn
University of Tubingen
Co-authored papers 47
Kevin K Jin
Cardiovascular Institute, Stanford University School of Medicine
Co-authored papers 47
Raymond C Stevens
iHuman Institute, ShanghaiTech University
Co-authored papers 46
Lian Duan
Brown University
Co-authored papers 46
Thomas Clayton
Celgene/Bristol-Myers Squibb Corporation
Co-authored papers 45
Linda Okach
Co-authored papers 45
Dennis Carlton
Co-authored papers 44
Release 1.2