Pratyush Tiwary - Publications

Affiliations: 
2017- Chemistry and Biochemistry University of Maryland, College Park, College Park, MD 
Area:
statistical mechanics, molecular dynamics, rare events, enhanced sampling, drug design
Website:
sites.google.com/site/pratyushtiwary/

39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Smith Z, Ravindra P, Wang Y, Cooley R, Tiwary P. Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 32841026 DOI: 10.1021/acs.jpcb.0c03985  0.48
2020 Wang Y, Tiwary P. Understanding the role of predictive time delay and biased propagator in RAVE. The Journal of Chemical Physics. 152: 144102. PMID 32295373 DOI: 10.1063/5.0004838  0.48
2020 Wang Y, Lamim Ribeiro JM, Tiwary P. Machine learning approaches for analyzing and enhancing molecular dynamics simulations. Current Opinion in Structural Biology. 61: 139-145. PMID 31972477 DOI: 10.1016/j.sbi.2019.12.016  0.48
2019 Wang Y, Ribeiro JML, Tiwary P. Past-future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. Nature Communications. 10: 3573. PMID 31395868 DOI: 10.1038/s41467-019-11405-4  0.48
2018 Ribeiro JML, Tsai ST, Pramanik D, Wang Y, Tiwary P. Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet? Biochemistry. PMID 30547565 DOI: 10.1021/acs.biochem.8b00977  0.48
2018 Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K. Frequency adaptive metadynamics for the calculation of rare-event kinetics. The Journal of Chemical Physics. 149: 072309. PMID 30134721 DOI: 10.1063/1.5024679  1
2018 Ribeiro JML, Bravo P, Wang Y, Tiwary P. Reweighted autoencoded variational Bayes for enhanced sampling (RAVE). The Journal of Chemical Physics. 149: 072301. PMID 30134694 DOI: 10.1063/1.5025487  0.48
2017 Tiwary P, Berne BJ. Predicting reaction coordinates in energy landscapes with diffusion anisotropy. The Journal of Chemical Physics. 147: 152701. PMID 29055314 DOI: 10.1063/1.4983727  1
2017 Tiwary P, Mondal J, Berne BJ. How and when does an anticancer drug leave its binding site? Science Advances. 3: e1700014. PMID 28580424 DOI: 10.1126/sciadv.1700014  1
2017 Casasnovas R, Limongelli V, Tiwary P, Carloni P, Parrinello M. Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations. Journal of the American Chemical Society. PMID 28290199 DOI: 10.1021/jacs.6b12950  1
2016 Salvalaglio M, Tiwary P, Maggioni GM, Mazzotti M, Parrinello M. Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations. The Journal of Chemical Physics. 145: 211925. PMID 28799374 DOI: 10.1063/1.4966265  1
2016 Tiwary P, Berne BJ. How wet should be the reaction coordinate for ligand unbinding? The Journal of Chemical Physics. 145: 054113. PMID 27497545 DOI: 10.1063/1.4959969  1
2016 Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. Journal of Chemical Theory and Computation. PMID 27145262 DOI: 10.1021/acs.jctc.6b00201  1
2016 Tiwary P, Berne BJ. Kramers turnover: From energy diffusion to spatial diffusion using metadynamics. The Journal of Chemical Physics. 144: 134103. PMID 27059558 DOI: 10.1063/1.4944577  1
2016 Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annual Review of Physical Chemistry. PMID 26980304 DOI: 10.1146/annurev-physchem-040215-112229  1
2016 Mondal J, Tiwary P, Berne BJ. How a kinase inhibitor withstands Gatekeeper residue mutations. Journal of the American Chemical Society. PMID 26954686 DOI: 10.1021/jacs.6b01232  1
2016 Tiwary P, Berne BJ. Spectral gap optimization of order parameters for sampling complex molecular systems. Proceedings of the National Academy of Sciences of the United States of America. PMID 26929365 DOI: 10.1073/pnas.1600917113  1
2015 Tiwary P, Dama JF, Parrinello M. A perturbative solution to metadynamics ordinary differential equation. The Journal of Chemical Physics. 143: 234112. PMID 26696051 DOI: 10.1063/1.4937945  1
2015 Fleming KL, Tiwary P, Pfaendtner J. A New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations. The Journal of Physical Chemistry. A. PMID 26690335 DOI: 10.1021/acs.jpca.5b10667  1
2015 Quhe R, Nava M, Tiwary P, Parrinello M. Path Integral Metadynamics. Journal of Chemical Theory and Computation. 11: 1383-8. PMID 26574350 DOI: 10.1021/ct501002a  1
2015 Nava M, Quhe R, Palazzesi F, Tiwary P, Parrinello M. de Broglie Swapping Metadynamics for Quantum and Classical Sampling. Journal of Chemical Theory and Computation. 11: 5114-9. PMID 26574309 DOI: 10.1021/acs.jctc.5b00818  1
2015 Tiwary P, Mondal J, Morrone JA, Berne BJ. Role of water and steric constraints in the kinetics of cavity-ligand unbinding. Proceedings of the National Academy of Sciences of the United States of America. PMID 26371312 DOI: 10.1073/pnas.1516652112  1
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation. Physical Review Letters. 115: 070601. PMID 26317704 DOI: 10.1103/PhysRevLett.115.070601  1
2015 Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps. Proceedings of the National Academy of Sciences of the United States of America. 112: E386-91. PMID 25605901 DOI: 10.1073/pnas.1424461112  1
2015 Tiwary P, Parrinello M. A time-independent free energy estimator for metadynamics. The Journal of Physical Chemistry. B. 119: 736-42. PMID 25046020 DOI: 10.1021/jp504920s  1
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation Physical Review Letters. 115. DOI: 10.1103/PhysRevLett.115.070601  1
2015 Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps Proceedings of the National Academy of Sciences of the United States of America. 112: E386-E391. DOI: 10.1073/pnas.1424461112  1
2015 Tiwary P, Parrinello M. A time-independent free energy estimator for metadynamics Journal of Physical Chemistry B. 119: 736-742. DOI: 10.1021/jp504920s  1
2015 Quhe R, Nava M, Tiwary P, Parrinello M. Path integral metadynamics Journal of Chemical Theory and Computation. 11: 1383-1388. DOI: 10.1021/ct501002a  1
2014 Salvalaglio M, Tiwary P, Parrinello M. Assessing the Reliability of the Dynamics Reconstructed from Metadynamics. Journal of Chemical Theory and Computation. 10: 1420-5. PMID 26580360 DOI: 10.1021/ct500040r  1
2014 Van De Walle A, Hong Q, Miljacic L, Gopal CB, Demers S, Pomrehn G, Kowalski A, Tiwary P. Ab initio calculation of anisotropic interfacial excess free energies Physical Review B - Condensed Matter and Materials Physics. 89. DOI: 10.1103/PhysRevB.89.184101  1
2014 Salvalaglio M, Tiwary P, Parrinello M. Assessing the reliability of the dynamics reconstructed from metadynamics Journal of Chemical Theory and Computation. 10: 1420-1425. DOI: 10.1021/ct500040r  1
2013 Tiwary P, Parrinello M. From metadynamics to dynamics. Physical Review Letters. 111: 230602. PMID 24476246 DOI: 10.1103/PhysRevLett.111.230602  1
2013 Tiwary P, Parrinello M. From metadynamics to dynamics Physical Review Letters. 111. DOI: 10.1103/PhysRevLett.111.230602  1
2013 Tiwary P, Van De Walle A. Accelerated molecular dynamics through stochastic iterations and collective variable based basin identification Physical Review B - Condensed Matter and Materials Physics. 87. DOI: 10.1103/PhysRevB.87.094304  1
2013 Van De Walle A, Tiwary P, De Jong M, Olmsted DL, Asta M, Dick A, Shin D, Wang Y, Chen LQ, Liu ZK. Efficient stochastic generation of special quasirandom structures Calphad: Computer Coupling of Phase Diagrams and Thermochemistry. 42: 13-18. DOI: 10.1016/j.calphad.2013.06.006  1
2011 Tiwary P, Van De Walle A. Hybrid deterministic and stochastic approach for efficient atomistic simulations at long time scales Physical Review B - Condensed Matter and Materials Physics. 84. DOI: 10.1103/PhysRevB.84.100301  1
2011 Tiwary P, Van De Walle A, Jeon B, Grønbech-Jensen N. Interatomic potentials for mixed oxide and advanced nuclear fuels Physical Review B - Condensed Matter and Materials Physics. 83. DOI: 10.1103/PhysRevB.83.094104  1
2009 Tiwary P, Van De Walle A, Grønbech-Jensen N. Ab initio construction of interatomic potentials for uranium dioxide across all interatomic distances Physical Review B - Condensed Matter and Materials Physics. 80. DOI: 10.1103/PhysRevB.80.174302  1
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