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1

Integrative, dynamic structural biology at atomic resolution—it's about time

van den Bedem, Henry, Fraser, James S

Journal:

Year:

2015

Language:

english

File:

PDF, 2.23 MB

english, 2015

2

Probing RNA Native Conformational Ensembles with Structural Constraints

Fonseca, Rasmus, van den Bedem, Henry, Bernauer, Julie

Journal:

Journal of Computational Biology

Year:

2016

Language:

english

File:

PDF, 504 KB

english, 2016

3

Automated identification of functional dynamic contact networks from X-ray crystallography

van den Bedem, Henry, Bhabha, Gira, Yang, Kun, Wright, Peter E, Fraser, James S

Journal:

Year:

2013

Language:

english

File:

PDF, 1.51 MB

english, 2013

4

Discovering and Manipulating Protein Conformational Heterogeneity and Function

Keedy, Daniel, van den Bedem, Henry, Rettenmaier, Justin, Wells, James, Fraser, James

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 137 KB

english, 2014

5

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

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

Journal:

Journal of the Mechanics and Physics of Solids

Year:

2015

Language:

english

File:

PDF, 4.02 MB

english, 2015

6

Tau-ism: The Yin and Yang of Microtubule Sliding, Detachment, and Rupture

van den Bedem, Henry, Kuhl, Ellen

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 559 KB

english, 2015

7

Accessing protein conformational ensembles using room-temperature X-ray crystallography

James S. Fraser, Henry van den Bedem, Avi J. Samelson, P. Therese Lang, James M. Holton, Nathaniel Echols and Tom Alber

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.53 MB

english, 2011

8

Coupled motions in β 2 AR:Gαs conformational ensembles

Pachov, Dimitar V., Fonseca, Rasmus, Arnol, Damien, Bernauer, Julie, van den Bedem, Henry

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 4.50 MB

english, 2016

9

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca 2+ -calmodulin

Lin, Jiusheng, van den Bedem, Henry, Brunger, Axel T., Wilson, Mark A.

Journal:

Acta Crystallographica Section D Structural Biology

Year:

2016

Language:

english

File:

PDF, 1.83 MB

english, 2016

10

Visualizing chaperone-assisted protein folding

Horowitz, Scott, Salmon, Loïc, 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,

Journal:

Nature Structural and Molecular Biology

Year:

2016

Language:

english

File:

PDF, 2.18 MB

english, 2016

11

A geometric approach to characterize rigidity in proteins

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

Journal:

Year:

2015

Language:

english

File:

PDF, 2.41 MB

english, 2015

12

Conformational variation of proteins at room temperature is not dominated by radiation damage

Russi, Silvia, González, Ana, Kenner, Lillian R., Keedy, Daniel A., Fraser, James S., van den Bedem, Henry

Journal:

Journal of Synchrotron Radiation

Year:

2017

Language:

english

File:

PDF, 325 KB

english, 2017

13

Molecular Mechanisms of Chronic Traumatic Encephalopathy

van den Bedem, Henry, Kuhl, Ellen

Journal:

Current Opinion in Biomedical Engineering

Year:

2017

Language:

english

File:

PDF, 4.79 MB

english, 2017

14

Frustration-Guided Motion Planning Reveals Conformational Transitions in Proteins

Budday, Dominik, Fonseca, Rasmus, Leyendecker, Sigrid, van den Bedem, Henry

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 21.92 MB

english, 2017

15

Fast, clash-free RNA conformational morphing using molecular junctions

Héliou, Amélie, Budday, Dominik, Fonseca, Rasmus, van den Bedem, Henry

Journal:

Year:

2017

Language:

english

File:

PDF, 851 KB

english, 2017

16

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

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

Journal:

Environmental Microbiology Reports

Year:

2017

Language:

english

File:

PDF, 910 KB

english, 2017

17

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

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

Journal:

Journal of Computational Chemistry

Year:

2018

Language:

english

File:

PDF, 1013 KB

english, 2018

18

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

Keedy, Daniel A., Fraser, James S., van den Bedem, Henry, Shehu, Amarda

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.23 MB

english, 2015

19

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

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

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 8.90 MB

english, 2018

20

Reply to ‘Misreading chaperone–substrate complexes from random noise’

Horowitz, Scott, Salmon, Loïc, 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

Journal:

Nature Structural and Molecular Biology

Year:

2018

Language:

english

File:

PDF, 677 KB

english, 2018

21

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

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

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 43 KB

english, 2018

22

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

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

Journal:

Journal of Medicinal Chemistry

Year:

2018

Language:

english

File:

PDF, 1.96 MB

english, 2018

23

[ACM Press the 8th ACM International Conference - Boston, Massachusetts, USA (2017.08.20-2017.08.23)] Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17 - Fast, Clash-Free RNA Conformational Morphing using Molecular Junctions

Heliou, A., Budday, Dominik, Fonseca, Rasmus, van den Bedem, Henry

Year:

2017

Language:

english

File:

PDF, 1.60 MB

english, 2017

24

Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution

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

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 1.23 MB

english, 2019

25

Molecular Recognition of M1-Linked Ubiquitin Chains by Native and Phosphorylated UBAN Domains

Herhaus, Lina, van den Bedem, Henry, Tang, Sean, Maslennikov, Innokentiy, Wakatsuki, Soichi, Dikic, Ivan, Rahighi, Simin

Journal:

Journal of Molecular Biology

Year:

2019

Language:

english

File:

PDF, 7.86 MB

english, 2019

26

Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation

van den Bedem, Henry, Wilson, Mark A

Journal:

Journal of Synchrotron Radiation

Year:

2019

Language:

english

File:

PDF, 1.21 MB

english, 2019

27

Transport Properties of Nanoporous, Chemically Forced Biological Lattices

Li, Ponan, Herrmann, Jonathan, Wakatsuki, Soichi, van den Bedem, Henry

Journal:

Journal of Physical Chemistry B

Year:

2019

Language:

english

File:

PDF, 7.83 MB

english, 2019

28

KinoâGeometric Modeling: Insights into Protein Molecular Mechanisms

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

Journal:

Year:

2019

File:

PDF, 3.83 MB

2019

29

qFit 3: Protein and ligand multiconformer modeling for Xâray crystallographic and singleâparticle cryoâEM density maps

Riley, Blake T., Wankowicz, Stephanie A., de Oliveira, Saulo H. P., van Zundert, Gydo C. P., Hogan, Daniel W., Fraser, James S., Keedy, Daniel A., van den Bedem, Henry

Journal:

Protein Science

Year:

2020

File:

PDF, 3.15 MB

2020

30

Modeling of hidden structures using sparse chemical shift data from NMR relaxation dispersion

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

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 221 KB

2020