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Henry van den Bedem
Henry van den Bedem
VP, ML Research & Cheminformatics, Atomwise Inc. and Dept of BTS, UCSF
Verified email at ucsf.edu
Title
Cited by
Cited by
Year
Accessing protein conformational ensembles using room-temperature X-ray crystallography
JS Fraser, H van den Bedem, AJ Samelson, PT Lang, JM Holton, ...
Proceedings of the National Academy of Sciences 108 (39), 16247-16252, 2011
4922011
Integrative, dynamic structural biology at atomic resolution—it's about time
H Van Den Bedem, JS Fraser
Nature methods 12 (4), 307-318, 2015
2112015
Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR
RB Fenwick, H van den Bedem, JS Fraser, PE Wright
Proceedings of the National Academy of Sciences 111 (4), E445-E454, 2014
1402014
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection
SM Soltis, AE Cohen, A Deacon, T Eriksson, A González, S McPhillips, ...
Acta Crystallographica Section D: Biological Crystallography 64 (12), 1210-1221, 2008
1332008
Automated diffraction image analysis and spot searching for high-throughput crystal screening
Z Zhang, NK Sauter, H Van Den Bedem, G Snell, AM Deacon
Journal of applied crystallography 39 (1), 112-119, 2006
1332006
Automated identification of functional dynamic contact networks from X-ray crystallography
H Van Den Bedem, G Bhabha, K Yang, PE Wright, JS Fraser
Nature methods 10 (9), 896-902, 2013
1312013
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography
DA Keedy, LR Kenner, M Warkentin, RA Woldeyes, JB Hopkins, ...
Elife 4, e07574, 2015
1292015
Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR
DA Keedy, H Van Den Bedem, DA Sivak, GA Petsko, D Ringe, MA Wilson, ...
Structure 22 (6), 899-910, 2014
1052014
Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
H Van Den Bedem, A Dhanik, JC Latombe, AM Deacon
Acta Crystallographica Section D: Biological Crystallography 65 (10), 1107-1117, 2009
1052009
Crystal structures of two novel dye‐decolorizing peroxidases reveal a β‐barrel fold with a conserved heme‐binding motif
C Zubieta, SS Krishna, M Kapoor, P Kozbial, D McMullan, HL Axelrod, ...
Proteins: Structure, Function, and Bioinformatics 69 (2), 223-233, 2007
902007
Identification and structural characterization of heme binding in a novel dye‐decolorizing peroxidase, TyrA
C Zubieta, R Joseph, S Sri Krishna, D McMullan, M Kapoor, HL Axelrod, ...
Proteins: Structure, Function, and Bioinformatics 69 (2), 234-243, 2007
822007
Structural basis of murein peptide specificity of a γ-D-glutamyl-L-diamino acid endopeptidase
Q Xu, S Sudek, D McMullan, MD Miller, B Geierstanger, DH Jones, ...
Structure 17 (2), 303-313, 2009
782009
Exposing hidden alternative backbone conformations in X-ray crystallography using qFit
DA Keedy, JS Fraser, H van den Bedem
PLoS computational biology 11 (10), e1004507, 2015
702015
Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 Å resolution
P Kuhn, SA Lesley, II Mathews, JM Canaves, LS Brinen, X Dai, ...
Proteins: Structure, Function, and Bioinformatics 49 (1), 142-145, 2002
702002
Real-space protein-model completion: an inverse-kinematics approach
H Van Den Bedem, I Lotan, JC Latombe, AM Deacon
Acta Crystallographica Section D: Biological Crystallography 61 (1), 2-13, 2005
692005
Structure 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 …
Q Xu, P Abdubek, T Astakhova, HL Axelrod, C Bakolitsa, X Cai, D Carlton, ...
Acta Crystallographica Section F: Structural Biology and Crystallization …, 2010
662010
Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold
C Rife, R Schwarzenbacher, D McMullan, P Abdubek, E Ambing, ...
Proteins: Structure, Function, and Bioinformatics 61 (2), 449-453, 2005
582005
Efficient algorithms to explore conformation spaces of flexible protein loops
P Yao, A Dhanik, N Marz, R Propper, C Kou, G Liu, H Van Den Bedem, ...
IEEE/ACM Transactions on Computational Biology and Bioinformatics 5 (4), 534-545, 2008
482008
Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair
D Das, D Moiani, HL Axelrod, MD Miller, D McMullan, KK Jin, P Abdubek, ...
Journal of molecular biology 397 (3), 647-663, 2010
462010
Conformational variation of proteins at room temperature is not dominated by radiation damage
S Russi, A González, LR Kenner, DA Keedy, JS Fraser, H Bedem
Journal of synchrotron radiation 24 (1), 73-82, 2017
452017
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