Release 5 June 2012 TraDES-2
2 Sept 2012 Beta Release of the TraDES R Analysis Package (attached at bottom of this web page)

TraDES was created in the Hogue Laboratory, formerly at the National University of Singapore, and Mount Sinai Hospital/Univeristy of Toronto.


Trajectory Directed Ensemble Sampling

Create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded.

TraDES is a system for directly controlling and sampling protein conformational space.

TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. 

Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments.

TODAY TraDES is a growing concern for scientists studying proteins that do not fold - intrinsically disordered proteins. 

NMR scientists are the primary users of the TraDES package.

TraDES Programs:

The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are:

  • trades - generates protein structures following the Trajectory Distribution (see below)
  • seq2trj - makes Trajectory Distributions from sequences for sampling
  • str2tr -  makes Trajectory Distributions from 3D structures for sampling

Trajectory Distributions - Controlling the Sampling of Conformational Space

The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue.
Read more....

Christopher Hogue,
Oct 1, 2012, 7:50 PM