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David E. Shaw
David E. Shaw
Bestätigte E-Mail-Adresse bei deshaw.com
Titel
Zitiert von
Zitiert von
Jahr
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
RA Friesner, JL Banks, RB Murphy, TA Halgren, JJ Klicic, DT Mainz, ...
Journal of medicinal chemistry 47 (7), 1739-1749, 2004
91952004
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
K Lindorff‐Larsen, S Piana, K Palmo, P Maragakis, JL Klepeis, RO Dror, ...
Proteins: Structure, Function, and Bioinformatics 78 (8), 1950-1958, 2010
54782010
Scalable algorithms for molecular dynamics simulations on commodity clusters
KJ Bowers, E Chow, H Xu, RO Dror, MP Eastwood, BA Gregersen, ...
Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, 84-es, 2006
29632006
A hierarchical approach to all‐atom protein loop prediction
MP Jacobson, DL Pincus, CS Rapp, TJF Day, B Honig, DE Shaw, ...
Proteins: Structure, Function, and Bioinformatics 55 (2), 351-367, 2004
22132004
How fast-folding proteins fold
K Lindorff-Larsen, S Piana, RO Dror, DE Shaw
Science 334 (6055), 517, 2011
20122011
Atomic-level characterization of the structural dynamics of proteins
DE Shaw, P Maragakis, K Lindorff-Larsen, S Piana, RO Dror, ...
Science 330 (6002), 341-346, 2010
20112010
PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
SL Dixon, AM Smondyrev, EH Knoll, SN Rao, DE Shaw, RA Friesner
Journal of computer-aided molecular design 20, 647-671, 2006
12842006
Biomolecular simulation: a computational microscope for molecular biology
RO Dror, RM Dirks, JP Grossman, H Xu, DE Shaw
Annual review of biophysics 41, 429-452, 2012
12192012
Anton, a special-purpose machine for molecular dynamics simulation
DE Shaw, MM Deneroff, RO Dror, JS Kuskin, RH Larson, JK Salmon, ...
Communications of the ACM 51 (7), 91-97, 2008
9632008
Long-timescale molecular dynamics simulations of protein structure and function
JL Klepeis, K Lindorff-Larsen, RO Dror, DE Shaw
Current opinion in structural biology 19 (2), 120-127, 2009
9182009
Structure and dynamics of the M3 muscarinic acetylcholine receptor
AC Kruse, J Hu, AC Pan, DH Arlow, DM Rosenbaum, E Rosemond, ...
Nature 482 (7386), 552-556, 2012
9082012
Structure and function of an irreversible agonist-β2 adrenoceptor complex
DM Rosenbaum, C Zhang, JA Lyons, R Holl, D Aragao, DH Arlow, ...
Nature 469 (7329), 236-240, 2011
9042011
The dynamic process of β2-adrenergic receptor activation
R Nygaard, Y Zou, RO Dror, TJ Mildorf, DH Arlow, A Manglik, AC Pan, ...
Cell 152 (3), 532-542, 2013
8812013
How robust are protein folding simulations with respect to force field parameterization?
S Piana, K Lindorff-Larsen, DE Shaw
Biophysical journal 100 (9), L47-L49, 2011
8512011
A detailed and flexible cycle-accurate network-on-chip simulator
N Jiang, DU Becker, G Michelogiannakis, J Balfour, B Towles, DE Shaw, ...
2013 IEEE international symposium on performance analysis of systems and …, 2013
8452013
Developing a molecular dynamics force field for both folded and disordered protein states
P Robustelli, S Piana, DE Shaw
Proceedings of the National Academy of Sciences 115 (21), E4758-E4766, 2018
8062018
Pathway and mechanism of drug binding to G-protein-coupled receptors
RO Dror, AC Pan, DH Arlow, DW Borhani, P Maragakis, Y Shan, H Xu, ...
Proceedings of the National Academy of Sciences 108 (32), 13118-13123, 2011
7982011
Systematic validation of protein force fields against experimental data
K Lindorff-Larsen, P Maragakis, S Piana, MP Eastwood, RO Dror, ...
PloS one 7 (2), e32131, 2012
7572012
Water dispersion interactions strongly influence simulated structural properties of disordered protein states
S Piana, AG Donchev, P Robustelli, DE Shaw
The journal of physical chemistry B 119 (16), 5113-5123, 2015
7232015
Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer
DE Shaw, JP Grossman, JA Bank, B Batson, JA Butts, JC Chao, ...
SC'14: Proceedings of the International Conference for High Performance …, 2014
6932014
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