New Release 5 June 2012 TraDES-2 Now Open Source! ftp://ftp.blueprint.org/pub/TraDES/
New 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, which is now hosted at the
Mechanobiology Institute of Singapore and the Dept. of Biological Sciences
at the National University of Singapore.

 

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.

Download TraDES here:
ftp://ftp.blueprint.org/pub/TraDES/

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....

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TraDES_R_Analysis_Package.r
(119k)
Christopher Hogue,
Oct 1, 2012, 7:50 PM