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URL: https://sites.google.com/a/blueprint.org/trades/
Proper Citation: TraDES (RRID:SCR_006142)
Description: With Trajectory Directed Ensemble Sampling (TraDES) 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. 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. NMR scientists are the primary users of the TraDES package.
Abbreviations: TraDES
Synonyms: Trajectory Directed Ensemble Sampling, TraDES - Trajectory Directed Ensemble Sampling
Resource Type: software resource, software application
Defining Citation: PMID:11746699, PMID:10737933
Keywords: protein, protein structure, structure, trajectory, sequence, protein folding
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Christopher Hogues Research Lab at the National University of Singapore |
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