Henry van den Bedem

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 20

Top Topics

Molecular Dynamics Simulations

Endoplasmic Reticulum

Top Venues

Journal of chemical information and modeling

Nature structural & molecular biology

bioRxiv : the preprint server for biology

This page only lists publications with an associated author ORCID identifier.

Publications

Henry van den Bedem
Microbes 'sieve' ions on their surface to start the nitrogen cycle. Nature 630 (8015) (2024)
Henry van den Bedem
Microbes 'sieve' ions on their surface to start the nitrogen cycle. Nature 630 (8015) (2024)
Henry van den Bedem
Microbes 'sieve' ions on their surface to start the nitrogen cycle. Nature (2024)
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake T Riley, Akshay Raju, Daniel W Hogan, Henry van den Bedem, Daniel A Keedy, Brian K Shoichet
Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv : the preprint server for biology (2023)
Artur Meller, Saulo de Oliveira, Aram Davtyan, Tigran M Abramyan, Gregory R Bowman, Henry van den Bedem
Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors. bioRxiv : the preprint server for biology (2023)
Kate A Stafford, Brandon M Anderson, Jon Sorenson, Henry van den Bedem
AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens. Journal of chemical information and modeling 62 (5) (2022)
Xiyu Chen, Sigrid Leyendecker, Henry van den Bedem
Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease. Journal of chemical information and modeling 62 (11) (2022)
Blake T Riley, Stephanie A Wankowicz, Saulo H P de Oliveira, Gydo C P van Zundert, Daniel W Hogan, Brian K Shoichet, Daniel A Keedy, Henry van den Bedem
qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein science : a publication of the Protein Society 30 (1) (2020)
Alexander M Wolff, Iris D Young, Raymond G Sierra, Aaron S Brewster, Michael W Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T Biel, Sergio Carbajo, Aina E Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D Koralek, Minoru Kubo, Tomas S Lazarou, Takashi Nomura, Shigeki Owada, Avi J Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M Thompson, Henry van den Bedem, Rahel A Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensure Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K Sauter, Brian K Shoichet, Michael C Thompson
Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ 7 (Pt 2) (2020)
Po-Nan Li, Jonathan Herrmann, Soichi Wakatsuki, Henry van den Bedem
Transport Properties of Nanoporous, Chemically Forced Biological Lattices. The journal of physical chemistry. B 123 (49) (2019)
Scott Horowitz, Loïc Salmon, Philipp Koldewey, Logan S Ahlstrom, Raoul Martin, Shu Quan, Pavel V Afonine, Henry van den Bedem, Lili Wang, Qingping Xu, Raymond C Trievel, Charles L Brooks, James C A Bardwell
Reply to 'Misreading chaperone-substrate complexes from random noise'. Nature structural & molecular biology 25 (11) (2019)
Kaiming Zhang, Huawei Zhang, Shanshan Li, Grigore D Pintilie, Tung-Chung Mou, Yuanzhu Gao, Qinfen Zhang, Henry van den Bedem, Michael F Schmid, Shannon Wing Ngor Au, Wah Chiu
Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution. Proceedings of the National Academy of Sciences of the United States of America 116 (14) (2019)
Henry van den Bedem, Mark A Wilson
Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. Journal of synchrotron radiation 26 (Pt 4) (2019)
Medhanjali Dasgupta, Dominik Budday, Saulo H P de Oliveira, Peter Madzelan, Darya Marchany-Rivera, Javier Seravalli, Brandon Hayes, Raymond G Sierra, Sébastien Boutet, Mark S Hunter, Roberto Alonso-Mori, Alexander Batyuk, Jennifer Wierman, Artem Lyubimov, Aaron S Brewster, Nicholas K Sauter, Gregory A Applegate, Virendra K Tiwari, David B Berkowitz, Michael C Thompson, Aina E Cohen, James S Fraser, Michael E Wall, Henry van den Bedem, Mark A Wilson
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 116 (51) (2019)
Dominik Budday, Sigrid Leyendecker, Henry van den Bedem
Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. Journal of chemical information and modeling 58 (10) (2018)
Rasmus Fonseca, Dominik Budday, Henry van den Bedem
Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces. Journal of computational chemistry 39 (12) (2018)
Gydo C P van Zundert, Brandi M Hudson, Saulo H P de Oliveira, Daniel A Keedy, Rasmus Fonseca, Amelie Heliou, Pooja Suresh, Kenneth Borrelli, Tyler Day, James S Fraser, Henry van den Bedem
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. Journal of medicinal chemistry 61 (24) (2018)
Po-Nan Li, Jonathan Herrmann, Bradley B Tolar, Frédéric Poitevin, Rasika Ramdasi, John R Bargar, David A Stahl, Grant J Jensen, Christopher A Francis, Soichi Wakatsuki, Henry van den Bedem
Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. The ISME journal 12 (10) (2018)
Dominik Budday, Rasmus Fonseca, Sigrid Leyendecker, Henry van den Bedem
Frustration-guided motion planning reveals conformational transitions in proteins. Proteins 85 (10) (2017)
Scott Horowitz, Loïc Salmon, Philipp Koldewey, Logan S Ahlstrom, Raoul Martin, Shu Quan, Pavel V Afonine, Henry van den Bedem, Lili Wang, Qingping Xu, Raymond C Trievel, Charles L Brooks, James C A Bardwell
Visualizing chaperone-assisted protein folding. Nature structural & molecular biology 23 (7) (2016)
Daniel A Keedy, Lillian R Kenner, Matthew Warkentin, Rahel A Woldeyes, Jesse B Hopkins, Michael C Thompson, Aaron S Brewster, Andrew H Van Benschoten, Elizabeth L Baxter, Monarin Uervirojnangkoorn, Scott E McPhillips, Jinhu Song, Roberto Alonso-Mori, James M Holton, William I Weis, Axel T Brunger, S Michael Soltis, Henrik Lemke, Ana Gonzalez, Nicholas K Sauter, Aina E Cohen, Henry van den Bedem, Robert E Thorne, Brian K Shoichet
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 4 (2015)