TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries

J Chem Inf Model. 2018 Nov 26;58(11):2178-2182. doi: 10.1021/acs.jcim.8b00512. Epub 2018 Oct 30.

Abstract

It is extremely helpful to be able to partition the thousands of frames produced in molecular dynamics simulations into a limited number of most dissimilar conformations. While robust clustering algorithms are already available to do so, there is a distinct need for an easy-to-use clustering program with complete user control, taking as input a trajectory from any molecular dynamics (MD) package and outputting an intuitive display of results with plots allowing at-a-glance analysis. We present TTClust (for Trusty Trajectory Clustering), a python program that uses the MDTraj package to fill this need.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cluster Analysis
  • Hepacivirus / chemistry
  • Hepacivirus / enzymology
  • Molecular Conformation
  • Molecular Dynamics Simulation*
  • Protein Conformation
  • Software*
  • Viral Nonstructural Proteins / chemistry

Substances

  • Viral Nonstructural Proteins
  • NS-5 protein, hepatitis C virus