Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics-Reference-Cited by-同舟云学术

Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics

Published:2015-09-21 Issue:11 Volume:143 Page:114109
ISSN:0021-9606
Container-title:The Journal of Chemical Physics
language:en
Short-container-title:The Journal of Chemical Physics

Author:

Chatterjee Abhijit¹,Bhattacharya Swati²

Affiliation:

1. Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India

2. Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, India

Funder

Department of Science and Technology, Ministry of Science and Technology (DST)

Publisher

AIP Publishing

Subject

Physical and Theoretical Chemistry,General Physics and Astronomy

Link

http://aip.scitation.org/doi/pdf/10.1063/1.4930976

Reference67 articles.

1. Peptide folding simulations

2. Molecular simulations of protein dynamics: new windows on mechanisms in biology

3. Escaping free-energy minima

4. D. E. Shaw, R. O. Dror, J. K. Salmon, J. P. Grossman, K. M. Mackenzie, J. A. Bank, C. Young, M. M. Deneroff, B. Batson, K. J. Bowers, E. Chow, M. P. Eastwood, D. J. Ierardi, J. L. Klepeis, J. S. Kuskin, R. H. Larson, K. Lindorff-Larsen, P. Maragakis, M. A. Moraes, S. Piana, Y. Shan, and B. Towles, “Millisecond-scale molecular dynamics simulations on Anton,” Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09) (ACM, New York, 2009).10.1063/1.1942487

5. Using generalized ensemble simulations and Markov state models to identify conformational states

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