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Kate Stafford
Kate Stafford
Director, Structural Cheminformatics, Atomwise
Verified email at atomwise.com
Title
Cited by
Cited by
Year
Efficient reversal of Alzheimer's disease fibril formation and elimination of neurotoxicity by a small molecule
BJ Blanchard, A Chen, LM Rozeboom, KA Stafford, P Weigele, VM Ingram
Proceedings of the National Academy of Sciences of the United States of …, 2004
1932004
Interpreting protein structural dynamics from NMR chemical shifts
P Robustelli, KA Stafford, AG Palmer III
Journal of the American Chemical Society 134 (14), 6365-6374, 2012
1332012
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
T Tu, CA Rendleman, DW Borhani, RO Dror, J Gullingsrud, MO Jensen, ...
High Performance Computing, Networking, Storage and Analysis, 2008. SC 2008 …, 2008
1072008
Automated event detection and activity monitoring in long molecular dynamics simulations
W Wriggers, KA Stafford, Y Shan, S Piana, P Maragakis, K Lindorff-Larsen, ...
Journal of Chemical Theory and Computation 5 (10), 2595-2605, 2009
592009
Thermostability of enzymes from molecular dynamics simulations
T Zeiske, KA Stafford, AG Palmer III
Journal of chemical theory and computation 12 (6), 2489-2492, 2016
522016
Equipartition and the calculation of temperature in biomolecular simulations
MP Eastwood, KA Stafford, RA Lippert, MØ Jensen, P Maragakis, ...
Journal of Chemical Theory and Computation 6 (7), 2045-2058, 2010
492010
Starting‐structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD‐derived order parameters
T Zeiske, KA Stafford, RA Friesner, AG Palmer III
Proteins: Structure, Function, and Bioinformatics 81 (3), 499-509, 2013
342013
Thermal adaptation of conformational dynamics in ribonuclease H
KA Stafford, P Robustelli, AG Palmer III
PLoS computational biology 9 (10), e1003218, 2013
322013
AtomNet PoseRanker: Enriching ligand pose quality for dynamic proteins in virtual high-throughput screens
KA Stafford, BM Anderson, J Sorenson, H Van Den Bedem
Journal of Chemical Information and Modeling 62 (5), 1178-1189, 2022
292022
Application of computer simulation free-energy methods to compute the free energy of micellization as a function of micelle composition. 2. Implementation
BC Stephenson, KA Stafford, KJ Beers, D Blankschtein
The Journal of Physical Chemistry B 112 (6), 1641-1656, 2008
212008
Side Chain Dynamics of Carboxyl and Carbonyl Groups in the Catalytic Function of Escherichia coli Ribonuclease H
KA Stafford, F Ferrage, JH Cho, AG Palmer III
Journal of the American Chemical Society 135 (48), 18024-18027, 2013
192013
Application of computer simulation free-energy methods to compute the free energy of micellization as a function of micelle composition. 1. Theory
BC Stephenson, KA Stafford, KJ Beers, D Blankschtein
The Journal of Physical Chemistry B 112 (6), 1634-1640, 2008
182008
Conformational preferences underlying reduced activity of a thermophilic ribonuclease H
KA Stafford, N Trbovic, JA Butterwick, R Abel, RA Friesner, AG Palmer III
Journal of molecular biology 427 (4), 853-866, 2015
142015
Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site
KA Stafford, AG Palmer III
F1000Research 3, 2014
102014
Stochastic pairwise alignments and scoring methods for comparative protein structure modeling
AC Marko, K Stafford, T Wymore
Journal of chemical information and modeling 47 (3), 1263-1270, 2007
102007
AI is a viable alternative to high throughput screening: a 318-target study
Scientific reports 14 (1), 7526, 2024
72024
Learning physics confers pose-sensitivity in structure-based virtual screening
P Gniewek, B Worley, K Stafford, H Bedem, B Anderson
arXiv preprint arXiv:2110.15459, 2021
72021
AI-predicted protein structures improve deep learning models for bioactivity prediction in drug discovery
H van den Bedem, S de Oliveira, K Stafford, C Rupakheti, A Rosnik
Journal of Biological Chemistry 299 (3), 103446, 2023
2023
Protein binding site fingerprinting for activity screening in machine learning
B Bergman, K Stafford, D Bernard, S Schroedl
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019
2019
Modeling protein flexibility with conformational sampling improves ligand pose and bioactivity prediction
K Stafford, J Sorenson, I Wallach
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019
2019
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Articles 1–20