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Rafal P. Wiewiora
Rafal P. Wiewiora
Principal, Molecular Design & Computational Biophysics, Psivant Therapeutics
Verified email at roivant.com - Homepage
Title
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Cited by
Year
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
20002017
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
2732016
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
253*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
1632020
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
502021
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
432019
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
322022
Ancestral reconstruction reveals mechanisms of ERK regulatory evolution
D Sang, S Pinglay, RP Wiewiora, ME Selvan, HJ Lou, JD Chodera, ...
eLife 8, 2019
282019
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
262021
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
122021
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
82015
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
32023
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
22018
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
STORMM: Structure and TOpology Replica Molecular Mechanics for chemical simulations
DS Cerutti, S Boothroyd, R Wiewiora, W Sherman
bioRxiv, 2024.03. 27.587048, 2024
2024
Citizen Scientists Create an Exascale Computer to Combat COVID-19 (preprint)
MI Zimmerman, JR Porter, MD Ward, S Singh, N Vithani, A Meller, ...
2020
Rigorous Construction of Markov State Models for Conformationally Selective Drug Design
RP Wiewiora
Weill Medical College of Cornell University, 2020
2020
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
Histone Lysine Methyltransferases-Conformational Dynamics and Selective Inhibitor Design for Chromatin-Modifying Enzymes in Lymphomas and Melanomas
R Wiewiora, ...
2018
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Articles 1–19