Enhanced sampling methods for atomistic simulation of nucleic acids

Catherine Kelso; Carlos Simmerling

doi:10.1007/978-1-4020-4851-3_6

Enhanced sampling methods for atomistic simulation of nucleic acids

Catherine Kelso
, Carlos Simmerling

Laufer Center for Physical and Quantitative Biology

Ward Melville High School
Stony Brook University

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

4 Scopus citations

Abstract

This review summarizes recent work in atomic-detail simulations of nucleic acids, with emphasis on methods to improve sampling of conformational ensembles, such as Locally Enhanced Sampling and Replica Exchange molecular dynamics. Studies of several model oligonucleotide systems are described in detail to compare these different approaches.

Original language	English
Title of host publication	Computational Studies of RNA and DNA
Publisher	Springer Netherlands
Pages	147-167
Number of pages	21
ISBN (Print)	1402048513, 9781402047947
DOIs	https://doi.org/10.1007/978-1-4020-4851-3_6
State	Published - 2006

Keywords

Free Energy Landscapes
Locally Enhanced Sampling
Parallel Tempering
Replica Exchange Method
Replica Exchange Molecular Dynamics

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10.1007/978-1-4020-4851-3_6

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title = "Enhanced sampling methods for atomistic simulation of nucleic acids",

abstract = "This review summarizes recent work in atomic-detail simulations of nucleic acids, with emphasis on methods to improve sampling of conformational ensembles, such as Locally Enhanced Sampling and Replica Exchange molecular dynamics. Studies of several model oligonucleotide systems are described in detail to compare these different approaches.",

keywords = "Free Energy Landscapes, Locally Enhanced Sampling, Parallel Tempering, Replica Exchange Method, Replica Exchange Molecular Dynamics",

author = "Catherine Kelso and Carlos Simmerling",

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AB - This review summarizes recent work in atomic-detail simulations of nucleic acids, with emphasis on methods to improve sampling of conformational ensembles, such as Locally Enhanced Sampling and Replica Exchange molecular dynamics. Studies of several model oligonucleotide systems are described in detail to compare these different approaches.

KW - Free Energy Landscapes

KW - Locally Enhanced Sampling

KW - Parallel Tempering

KW - Replica Exchange Method

KW - Replica Exchange Molecular Dynamics

UR - https://www.scopus.com/pages/publications/84876503328

U2 - 10.1007/978-1-4020-4851-3_6

DO - 10.1007/978-1-4020-4851-3_6

M3 - Chapter

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SN - 9781402047947

SP - 147

EP - 167

BT - Computational Studies of RNA and DNA

PB - Springer Netherlands

ER -

Enhanced sampling methods for atomistic simulation of nucleic acids

Abstract

Keywords

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