| OpenMM 7: Rapid development of high performance algorithms for molecular dynamics P Eastman, J Swails, JD Chodera, RT McGibbon, Y Zhao, KA Beauchamp, ... PLoS computational biology 13 (7), e1005659, 2017 | 2072 | 2017 |
| Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity TH Wright, BJ Bower, JM Chalker, GJL Bernardes, R Wiewiora, WL Ng, ... Science 354 (6312), aag1465, 2016 | 275 | 2016 |
| SARS-CoV-2 simulations go exascale to capture spike opening and reveal cryptic pockets across the proteome MI Zimmerman, G Bowman Biophysical Journal 120 (3), 299a, 2021 | 263* | 2021 |
| Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems P Gkeka, G Stoltz, A Barati Farimani, Z Belkacemi, M Ceriotti, JD Chodera, ... Journal of chemical theory and computation 16 (8), 4757-4775, 2020 | 168 | 2020 |
| What Markov state models can and cannot do: Correlation versus path-based observables in protein-folding models E Suárez, RP Wiewiora, C Wehmeyer, F Noé, JD Chodera, ... Journal of chemical theory and computation 17 (5), 3119-3133, 2021 | 50 | 2021 |
| The dynamic conformational landscape of the protein methyltransferase SETD8 S Chen, RP Wiewiora, F Meng, N Babault, A Ma, W Yu, K Qian, H Hu, ... Elife 8, e45403, 2019 | 44 | 2019 |
| Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Nature communications 13 (1), 5884, 2022 | 34 | 2022 |
| Ancestral reconstruction reveals mechanisms of ERK regulatory evolution D Sang, S Pinglay, RP Wiewiora, ME Selvan, HJ Lou, JD Chodera, ... eLife 8, 2019 | 29 | 2019 |
| Site-specific lipidation enhances IFITM3 membrane interactions and antiviral activity EH Garst, H Lee, T Das, S Bhattacharya, A Percher, R Wiewiora, IP Witte, ... ACS chemical biology 16 (5), 844-856, 2021 | 26 | 2021 |
| Atomic-resolution prediction of degrader-mediated ternary complex structures by combining molecular simulations with hydrogen deuterium exchange T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Biorxiv, 2021.09. 26.461830, 2021 | 12 | 2021 |
| An efficient one-pot synthesis of 2-bromo-6-aryl [5H] pyrrolo [2, 3-b] pyrazines I Simpson, SA St-Gallay, S Stokes, DTE Whittaker, R Wiewiora Tetrahedron Letters 56 (12), 1492-1495, 2015 | 8 | 2015 |
| Molecular Latent Space Simulators for Distributed and Multimolecular Trajectories MS Jones, ZA McDargh, RP Wiewiora, JA Izaguirre, H Xu, AL Ferguson The Journal of Physical Chemistry A 127 (25), 5470-5490, 2023 | 3 | 2023 |
| Conformational Dynamics of Histone Methyltransferase SET8 Probed by Millisecond-Timescale Molecular Dynamics, Markov State Modeling and Biochemical Experiments RP Wiewiora, S Chen, M Luo, JD Chodera Biophysical Journal 114 (3), 398a, 2018 | 2 | 2018 |
| Rigorous Construction of Markov State Models for Conformationally Selective Drug Design RP Wiewiora Weill Medical College of Cornell University, 2020 | 1 | 2020 |
| STORMM: Structure and topology replica molecular mechanics for chemical simulations DS Cerutti, R Wiewiora, S Boothroyd, W Sherman The Journal of Chemical Physics 161 (3), 2024 | | 2024 |
| Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design Y Qiu, RP Wiewiora, JA Izaguirre, H Xu, W Sherman, W Tang, X Huang | | 2024 |
| Markov models of functional dynamics of histone methyltransferases by millisecond-timescale molecular simulation and chemical probing R Wiewiora, S Chen, M Luo, J Chodera ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258, 2019 | | 2019 |
John D. ChoderaMemorial Sloan-Kettering Cancer CenterVerified email at mskcc.org
