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. It can be either a Ramachandran plot with a 3rd axis which indicates the frequency or probability at that point, or it can be in a spherical form indicating placement of alpha-carbons.
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VisTraj is a GUI tool to inspect and alter the conformational space sampling at each amino acid residue. It can be directed to sample broad swaths of conformational space or precise points. With VisTraj you can constrain the sampling of conformational space to exact helices or recapitulate the backbone conformation of a protein-binding motif.
Any protein has a sequence of trajectory distributions, each one representing the conformational space at each residue in the protein sequence.
Make a Trajectory File, Then Sample Conformational Space/Make Proteins
InitTraj, Val2Trj or UnfoldTraj are scripts that will generate an initial set of trajectory distributions using the included trajectory distribution dictionaries.
You can start with a FASTA formatted sequence.
The sampling program foldtraj takes as its input an ASN.1 trajectory distribution file
generated by InitTraj, Val2Trj, UnfoldTraj, or VisTraj.
The output will be a random all-atom conformer of the protein represented by theinput file. If derived from a crystal structure, it will atempt to
reconstruct the protein using only the C-alpha trajectory information.
In the TraDES package, a trajectory distribution file (ending in .trj or .trj.bz2) is a trajectory distribution sequence as well as global parameters describing the space and optionally a set of protein fragments that are included in the sampling. A trajectory distribution file is needed to sample conformational space of a given protein, and can be created from:
*Note that VisTraj is not supported on some operating systems. A *.trj file made by VisTraj or maketrj on one platform will work on any other.
For stability reasons we recommend using the Microsoft Windows version of VisTraj for creating *.trj files interactively, and then you can send the resulting *.trj file to your cluster running GNU/Linux or MacOS X.