TRAJELIX: a computational tool for the geometric characterization of protein helices during molecular dynamics simulations

J Comput Aided Mol Des. 2006 Feb;20(2):97-107. doi: 10.1007/s10822-006-9039-1. Epub 2006 May 10.


We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework ( that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs.

MeSH terms

  • Algorithms
  • Computer Simulation
  • Membrane Proteins / chemistry
  • Models, Molecular*
  • Protein Conformation
  • Protein Structure, Secondary*
  • Rhodopsin / chemistry
  • Software*


  • Membrane Proteins
  • Rhodopsin