Pratyush Tiwary
Pratyush Tiwary
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Cited by
Cited by
Efficient stochastic generation of special quasirandom structures
A Van de Walle, P Tiwary, M De Jong, DL Olmsted, M Asta, A Dick, D Shin, ...
Calphad 42, 13-18, 2013
Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint
O Valsson, P Tiwary, M Parrinello
Annu. Rev. Phys. Chem 67 (1), 159-184, 2016
Promoting transparency and reproducibility in enhanced molecular simulations
Nature methods 16 (8), 670-673, 2019
From metadynamics to dynamics
P Tiwary, M Parrinello
Physical review letters 111 (23), 230602, 2013
A time-independent free energy estimator for metadynamics
P Tiwary, M Parrinello
The Journal of Physical Chemistry B 119 (3), 736-742, 2015
Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
P Tiwary, V Limongelli, M Salvalaglio, M Parrinello
Proceedings of the National Academy of Sciences 112 (5), E386-E391, 2015
Spectral gap optimization of order parameters for sampling complex molecular systems
P Tiwary, BJ Berne
Proceedings of the National Academy of Sciences 113 (11), 2839-2844, 2016
Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)
JML Ribeiro, P Bravo, Y Wang, P Tiwary
The Journal of chemical physics 149 (7), 072301, 2018
Assessing the reliability of the dynamics reconstructed from metadynamics
M Salvalaglio, P Tiwary, M Parrinello
Journal of chemical theory and computation 10 (4), 1420-1425, 2014
Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations
R Casasnovas, V Limongelli, P Tiwary, P Carloni, M Parrinello
Journal of the American Chemical Society 139 (13), 4780-4788, 2017
Prediction of protein–ligand binding poses via a combination of induced fit docking and metadynamics simulations
AJ Clark, P Tiwary, K Borrelli, S Feng, EB Miller, R Abel, RA Friesner, ...
Journal of chemical theory and computation 12 (6), 2990-2998, 2016
Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics
Y Wang, JML Ribeiro, P Tiwary
Nature communications 10 (1), 1-8, 2019
Machine learning approaches for analyzing and enhancing molecular dynamics simulations
Y Wang, JML Ribeiro, P Tiwary
Current opinion in structural biology 61, 139-145, 2020
How and when does an anticancer drug leave its binding site?
P Tiwary, J Mondal, BJ Berne
Science advances 3 (5), e1700014, 2017
Role of water and steric constraints in the kinetics of cavity–ligand unbinding
P Tiwary, J Mondal, JA Morrone, BJ Berne
Proceedings of the National Academy of Sciences 112 (39), 12015-12019, 2015
Toward achieving efficient and accurate ligand-protein unbinding with deep learning and molecular dynamics through RAVE
JM Lamim Ribeiro, P Tiwary
Journal of chemical theory and computation 15 (1), 708-719, 2018
New approach for investigating reaction dynamics and rates with ab initio calculations
KL Fleming, P Tiwary, J Pfaendtner
The Journal of Physical Chemistry A 120 (2), 299-305, 2016
Frequency adaptive metadynamics for the calculation of rare-event kinetics
Y Wang, O Valsson, P Tiwary, M Parrinello, K Lindorff-Larsen
The Journal of chemical physics 149 (7), 072309, 2018
Learning molecular dynamics with simple language model built upon long short-term memory neural network
ST Tsai, EJ Kuo, P Tiwary
Nature communications 11 (1), 1-11, 2020
Kinetics of ligand binding through advanced computational approaches: a review
A Dickson, P Tiwary, H Vashisth
Current topics in medicinal chemistry 17 (23), 2626-2641, 2017
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