| 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 | 198 | 2004 |
| 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 | 132 | 2012 |
| 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 | 105 | 2008 |
| 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 | 58 | 2009 |
| 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 | 50 | 2016 |
| 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 | 48 | 2010 |
| 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 | 33 | 2013 |
| Thermal adaptation of conformational dynamics in ribonuclease H KA Stafford, P Robustelli, AG Palmer III PLoS computational biology 9 (10), e1003218, 2013 | 30 | 2013 |
| 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 | 26 | 2022 |
| 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 | 21 | 2008 |
| 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 | 18 | 2013 |
| 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 | 18 | 2008 |
| 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 | 12 | 2015 |
| 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 | 10 | 2007 |
| Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site KA Stafford, AG Palmer III F1000Research 3, 2014 | 9 | 2014 |
| 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 | 6 | 2021 |
| AI is a viable alternative to high throughput screening: a 318-target study Scientific Reports 14 (1), 7526, 2024 | 1 | 2024 |
| 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), S216, 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 |
