Henry van den Bedem - Publications, H-index & Citations

Henry van den Bedem

Stanford University

34H指数

267论文数

4.9K被引数

收录论文 86

发表时间

NGT: Generative AI with Synthesizability Guarantees Discovers MC2R Inhibitors from a Tera-Scale Virtual Screen

JOURNAL OF MEDICINAL CHEMISTRY

IF6.8

2024-10-29

PREAI

de Oliveira, Saulo H. P.; Pedawi, Aryan; Kenyon, Victor; van den Bedem, Henry

Automated multiconformer model building for X-ray crystallography and cryo-EM 用于x射线晶体学和cryo-em的自动多构象模型构建

ELIFE

IF0

2024-06-21

OAAI

Wankowicz, Stephanie A.; Ravikumar, Ashraya; Sharma, Shivani; Riley, Blake; Raju, Akshay; Hogan, Daniel W.; Flowers, Jessica; van den Bedem, Henry; Keedy, Daniel A.; Fraser, James S.

SARS-CoV-2 main protease mutation analysis via a kinematic method

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2023-07-05

OAAI

Chen, Xiyu; Leyendecker, Sigrid; van den Bedem, Henry

Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors

FRONTIERS IN MOLECULAR BIOSCIENCES

IF4

2023-04-18

OAAI

Meller, Artur; De Oliveira, Saulo; Davtyan, Aram; Abramyan, Tigran; Bowman, Gregory R.; van den Bedem, Henry

AI-predicted protein structures improve deep learning models for bioactivity prediction in drug discovery

JOURNAL OF BIOLOGICAL CHEMISTRY

IF3.9

2023-01-01

OAAI

van den Bedem, Henry; de Oliveira, Saulo; Stafford, Kate; Rupakheti, Chetan; Rosnik, Andreana

Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease

JOURNAL OF CHEMICAL INFORMATION AND MODELING

IF5.3

2022-05-20

PREAI

Chen, Xiyu; Leyendecker, Sigrid; van den Bedem, Henry

Ligand binding remodels protein side-chain conformational heterogeneity 配体结合重塑蛋白质侧链构象异质性

ELIFE

IF0

2022-03-21

OAAI

Wankowicz, Stephanie A.; de Oliveira, Saulo H.; Hogan, Daniel W.; van den Bedem, Henry; Fraser, James S.

AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens

JOURNAL OF CHEMICAL INFORMATION AND MODELING

IF5.3

2022-03-02

OAAI

Stafford, Kate A.; Anderson, Brandon M.; Sorenson, Jon; van den Bedem, Henry

Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion

BIOPHYSICAL JOURNAL

IF3.1

2021-01-01

OAAI

Fenwick, R. Bryn; Oyen, David; van den Bedem, Henry; Dyson, H. Jane; Wright, Peter E.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2019-12-04

OAAI

Dasgupta, Medhanjali; Budday, Dominik; de Oliveira, Saulo H. P.; Madzelan, Peter; Marchany-Rivera, Darya; Seravalli, Javier; Hayes, Brandon; Sierra, Raymond G.; Boutet, Sebastien; Hunter, Mark S.; Alonso-Mori, Roberto; Batyuk, Alexander; Wierman, Jennifer; Lyubimov, Artem; Brewster, Aaron S.; Sauter, Nicholas K.; Applegate, Gregory A.; Tiwari, Virendra K.; Berkowitz, David B.; Thompson, Michael C.; Cohen, Aina E.; Fraser, James S.; Wall, Michael E.; van den Bedem, Henry; Wilson, Mark A.

Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution 近原子分辨率下幽门螺杆菌空泡化细胞毒素A寡聚组装体的cryo-em结构

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2019-03-20

OAAI

Zhang, Kaiming; Zhang, Huawei; Li, Shanshan; Pintilie, Grigore D.; Mou, Tung-Chung; Gao, Yuanzhu; Zhang, Qinfen; van den Bedeme, Henry; Schmid, Michael F.; Au, Shannon Wing Ngor; Chiu, Wah

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps

JOURNAL OF MEDICINAL CHEMISTRY

IF6.8

2018-11-20

OAAI

van Zundert, Gydo C. P.; Hudson, Brandi M.; de Oliveira, Saulo H. P.; Keedy, Daniel A.; Fonseca, Rasmus; Heliou, Amelie; Suresh, Pooja; Borrelli, Kenneth; Day, Tyler; Fraser, James S.; van den Bedem, Henry

Reply to 'Misreading chaperone-substrate complexes from random noise'

NATURE STRUCTURAL & MOLECULAR BIOLOGY

IF10.1

2018-10-08

PREAI

Horowitz, Scott; Salmon, Loic; Koldewey, Philipp; Ahlstrom, Logan S.; Martin, Raoul; Quan, Shu; Afonine, Pavel V.; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C.; Brooks, Charles L., III; Bardwell, James C. A.

Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion

JOURNAL OF CHEMICAL INFORMATION AND MODELING

IF5.3

2018-09-21

OAAI

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins

ISME JOURNAL

IF10

2018-06-13

OAAI

Li, Po-Nan; Herrmann, Jonathan; Tolar, Bradley B.; Poitevin, Frederic; Ramdasi, Rasika; Bargar, John R.; Stahl, David A.; Jensen, Grant J.; Francis, Christopher A.; Wakatsuki, Soichi; van den Bedem, Henry

Cryo Electron Tomography and Reaction-Diffusion Simulations Reveal a Molecular and Evolutionary Basis for Charged Archaeal Surface Layer Proteins

BIOPHYSICAL JOURNAL

IF3.1

2018-02-01

OAAI

Li, Po-Nan; Herrmann, Jonathan R.; Poitevin, Frederic P. B.; Ramdasi, Rasika; Tolar, Bradley B.; Barger, John; Stahl, David; Jensen, Grant; Wakatsuki, Soichi; van den Bedem, Henry

Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces

JOURNAL OF COMPUTATIONAL CHEMISTRY

IF4.8

2018-01-05

OAAI

Fonseca, Rasmus; Budday, Dominik; van den Bedem, Henry

Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea

ENVIRONMENTAL MICROBIOLOGY REPORTS

IF2.7

2017-07-21

OAAI

Tolar, Bradley B.; Herrmann, Jonathan; Bargar, John R.; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A.