☰

Dhiman Ray - Publications

Affiliations: 
University of California, Irvine, Irvine, CA 
Area:
Theoretical Chemistry, Computational Biophysics
Tree Info Similar researchers PubMed Report error

13 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
2023 Ray D, Parrinello M. Kinetics from Metadynamics: Principles, Applications, and Outlook. Journal of Chemical Theory and Computation. PMID 37585703 DOI: 10.1021/acs.jctc.3c00660  0.386
2023 Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, et al. A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]. Living Journal of Computational Molecular Science. 5. PMID 37200895 DOI: 10.33011/livecoms.5.1.1655  0.599
2023 Prabhakar PR, Ray D, Andricioaei I. Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach. The Journal of Chemical Physics. 158: 134108. PMID 37031148 DOI: 10.1063/5.0140113  0.602
2022 Ray D, Ansari N, Rizzi V, Invernizzi M, Parrinello M. Rare Event Kinetics from Adaptive Bias Enhanced Sampling. Journal of Chemical Theory and Computation. PMID 36194840 DOI: 10.1021/acs.jctc.2c00806  0.339
2022 Stone SE, Ray D, Andricioaei I. Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. Journal of Chemical Information and Modeling. PMID 36049242 DOI: 10.1021/acs.jcim.2c00519  0.592
2022 Ray D, Quijano RN, Andricioaei I. Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies. Chemical Science. 13: 7224-7239. PMID 35799828 DOI: 10.1039/d2sc00534d  0.511
2021 Ray D, Stone SE, Andricioaei I. Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories. Journal of Chemical Theory and Computation. PMID 34910499 DOI: 10.1021/acs.jctc.1c00803  0.596
2021 Ray D, Le L, Andricioaei I. Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34615730 DOI: 10.1073/pnas.2100943118  0.564
2020 Ray D, Gokey T, Mobley DL, Andricioaei I. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning. The Journal of Chemical Physics. 153: 154117. PMID 33092382 DOI: 10.1063/5.0021953  0.594
2020 Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophysical Journal. PMID 32946766 DOI: 10.1016/J.Bpj.2020.08.031  0.606
2020 Liang D, Dahal U, Zhang YK, Lochbaum C, Ray D, Hamers RJ, Pedersen JA, Cui Q. Interfacial water and ion distribution determine potential and binding affinity of nanoparticles to biomolecules. Nanoscale. PMID 32852025 DOI: 10.1039/D0Nr03792C  0.325
2020 Ray D, Andricioaei I. Weighted ensemble milestoning (WEM): A combined approach for rare event simulations. The Journal of Chemical Physics. 152: 234114. PMID 32571033 DOI: 10.1063/5.0008028  0.619
2020 Ray D, Andricioaei I. Hoogsteen Base Pairing in DNA vs RNA: Thermodynamics and Kinetics from Enhanced Sampling Simulation and Markov State Modeling Biophysical Journal. 118: 299a-300a. DOI: 10.1016/J.Bpj.2019.11.1697  0.582
Show low-probability matches.