Dynamical Fragment Library

We generated fragment libraries from 2 ns snapshots of 298K simulations from a previous snapshot of the Dynameomics database. Each snapshot was fragmented using a sliding window along the entire length of the protein. The total number of fragments (and other characteristic information) for each library (a library consisting of fragments of a given length) are listed in Table 1. Seven libraries were generated, one for each fragment length of 3-9 residues, designated F3-F9.

The libraries are in a preliminary state. We are currently rebuilding libraries from the full Dynameomics dataset. The libraries will be constructed using OLAP in the Microsoft SQL Server Database. We anticipate that this will enable easier construction and maintenance of the libraries as well as allowing more detailed analyses.

Details on the construction of the fragment libraries are available in the Methods. The fragments have been separated into bins according to the distances between atoms in the terminal residues. These atoms are Cβ-Cβ and O-N for most fragment lengths. The exception is length 3: Cβ-C and O-N. Fragments were then clustered together to reduce the size of each bin to 200 fragments. These condensed libraries are available for download below. Fragments are contained in separate pdb files.