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DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling.
Ojha, Anupam Anand; Thakur, Saumya; Ahn, Surl-Hee; Amaro, Rommie E.
Afiliação
  • Ojha AA; Department of Chemistry, University of California San Diego, La Jolla, California92093, United States.
  • Thakur S; Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra400076, India.
  • Ahn SH; Department of Chemical Engineering, University of California Davis, Davis, California95616, United States.
  • Amaro RE; Department of Chemistry, University of California San Diego, La Jolla, California92093, United States.
J Chem Theory Comput ; 19(4): 1342-1359, 2023 Feb 28.
Article em En | MEDLINE | ID: mdl-36719802
Recent advances in computational power and algorithms have enabled molecular dynamics (MD) simulations to reach greater time scales. However, for observing conformational transitions associated with biomolecular processes, MD simulations still have limitations. Several enhanced sampling techniques seek to address this challenge, including the weighted ensemble (WE) method, which samples transitions between metastable states using many weighted trajectories to estimate kinetic rate constants. However, initial sampling of the potential energy surface has a significant impact on the performance of WE, i.e., convergence and efficiency. We therefore introduce deep-learned kinetic modeling approaches that extract statistically relevant information from short MD trajectories to provide a well-sampled initial state distribution for WE simulations. This hybrid approach overcomes any statistical bias to the system, as it runs short unbiased MD trajectories and identifies meaningful metastable states of the system. It is shown to provide a more refined free energy landscape closer to the steady state that could efficiently sample kinetic properties such as rate constants.

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: J Chem Theory Comput Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: J Chem Theory Comput Ano de publicação: 2023 Tipo de documento: Article