Literature DB >> 17280173

Bayesian update method for adaptive weighted sampling.

Sanghyun Park1, Daniel L Ensign, Vijay S Pande.   

Abstract

Exploring conformational spaces is still a challenging task for simulations of complex systems. One way to enhance such a task is weighted sampling, e.g., by assigning high weights to regions that are rarely sampled. It is, however, difficult to estimate adequate weights beforehand, and therefore adaptive methods are desired. Here we present a method for adaptive weighted sampling based on Bayesian inference. Within the framework of Bayesian inference, we develop an update scheme in which the information from previous data is stored in a prior distribution which is then updated to a posterior distribution according to new data. The method proposed here is particularly well suited for distributed computing, in which one must deal with rapid influxes of large amounts of data.

Year:  2006        PMID: 17280173     DOI: 10.1103/PhysRevE.74.066703

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  5 in total

1.  Statistically optimal analysis of samples from multiple equilibrium states.

Authors:  Michael R Shirts; John D Chodera
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

2.  Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

Authors:  Xuhui Huang; Gregory R Bowman; Vijay S Pande
Journal:  J Chem Phys       Date:  2008-05-28       Impact factor: 3.488

3.  Using Markov state models to study self-assembly.

Authors:  Matthew R Perkett; Michael F Hagan
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

4.  Pathways for virus assembly around nucleic acids.

Authors:  Jason D Perlmutter; Matthew R Perkett; Michael F Hagan
Journal:  J Mol Biol       Date:  2014-07-16       Impact factor: 5.469

5.  A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel.

Authors:  V A Voelz; P Petrone; V S Pande
Journal:  Pac Symp Biocomput       Date:  2009
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.