Dynameomics Fragment Library
Our fragment libraries were created to identify, rank and retrieve protein structure fragments
from both the Dynameomics data warehouse and Protein Data Bank (PDB) for protein loop structure
prediction. Dynameomics fragment structures supplement crystal structure fragment conformations
to improve loop predictions without being dependent on sequence homology. The fragment libraries
are accessible either through our web interface or via web services. Each of these methods is
described in detail below.
Web Interface
Our web interface was designed to generate backbone predictions for proteins from 3 to 22 residues
in length. Queries can be performed on our fragment libraries generated from Dynameomics or PDB
structures, containing approximately one billion fragment samples. Details of our library structure,
search methods, and evaluations have been submitted for publication as referenced below.
The interface supports queries using PDB codes or custom PDB formatted text files. Queries can be
performed on any one of the libraries individually or on a collection of libraries simultaneously.
We also integrated our rotamer library into the search mechanism, so side-chain structures can be
predicted along with the backbone structure by providing the appropriate sequence. Otherwise, backbone
structures will be provided as all alanine residues. Select the link below to use the web interface.
Fragment Search Web Interface
Web Services
We also provide programmatic access to the fragment libraries using web services. A sample Microsoft
.NET project is provided via the link below and includes a detailed example of using the fragment web
services. The web service methods provide a minimum interface to our libraries by exposing the internal
coordinates search method.
Fragment Web Service Example
Direct Web Service Access
If you have any questions regarding the DIVE software, email us at
dynameomics_info@uw.edu.
Reference List
- Rysavy SJ, Beck DAC, and Daggett V. Dynameomics: Data-driven Methods and
Models for Utilizing Large-Scale Protein Structure Repositories for Improving Fragment-Based Loop Prediction.
Submitted for publication, 2014.