Login / Signup

Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins.

Rodrigo Cossio-PérezJuliana PalmaGustavo Pierdominici-Sottile
Published in: Journal of chemical information and modeling (2017)
Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
Keyphrases
  • molecular dynamics simulations
  • molecular docking
  • depressive symptoms
  • electronic health record
  • molecular dynamics
  • machine learning
  • big data