Using Data-Reduction Techniques to Analyze Biomolecular Trajectories

Gareth A. Tribello*, Piero Gasparotto

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first part discusses how these various algorithms function as well as practical issues such as landmark selection and how these algorithms can be used when the data to be analyzed comes from enhanced sampling trajectories. In the later part a comparison between the results obtained by applying various algorithms to two sets of sample data is performed and discussed. This section is then followed by a summary of how one algorithm in particular, sketch-map, has been applied to a range of problems. The chapter concludes with a discussion on the directions that we believe this field is currently moving.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.,U.S.
Pages453-502
Number of pages50
DOIs
Publication statusPublished - 01 Jul 2019

Publication series

NameMethods in Molecular Biology
Volume2022
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Data analysis
  • Dimensionality reduction
  • Molecular dynamics
  • Sketch-map

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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