Wordom: a program for efficient analysis of molecular dynamics simulations

Bioinformatics. 2007 Oct 1;23(19):2625-7. doi: 10.1093/bioinformatics/btm378. Epub 2007 Aug 23.

Abstract

Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules and efficient handling of large sets of trajectories.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computer Simulation
  • Database Management Systems
  • Databases, Protein*
  • Information Storage and Retrieval / methods*
  • Models, Chemical*
  • Models, Molecular*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Software*
  • User-Computer Interface

Substances

  • Proteins