Library Code
Stable Release
The current stable release of EGAD Library is version 1.1. It is distributed as an archive of source code that can be compiled on multiple platforms:
Compilation instructions for different platforms can be found in the manual.
Development Sources
A publically accessible Subversion repository holds the most recent development release of EGAD Library. It can be found at:
https://pandemonium.ucsd.edu/svn/EGAD_Lib/
Be aware that the Subversion repository may contain broken code, as it is used during development of the software.
PyEGADLib Bindings
Python bindings for many of the classes in EGAD Library have been developed. They are distributed as a single module using the well-known distutils method. Compiling using distuils will also require a working compilation of the latest stable EGAD Library code.
| PyEGADLib-1.0.tgz | Distutils Source Distribution (platform independent) |
| PyEGADLib-1.0.win32-py2.4.exe | Windows Installer (Python 2.4) |
| PyEGADLib-1.0.win32-py2.4.zip | Windows Archive (Python 2.4, no installer) |
As users on different platforms contribute distributions, they will be posted here. Until one becomes available for your platform, you'll just have to compile it using distutils. If you have compiled a binary distribution of PyEGADLib not present here, please let us know!
Input Files
Most design applications require input files to specify the important parameters associated with a given forcefield. EGAD Library was developed using the OPLS forcefield. A set of default input files that employ this forcefield are provided:
Applications
Interaction Viewer
Interaction Viewer is a plug-in for PyMOL, the molecular visualization tool from DeLano Scientific. It provides the ability to calculate pairwise energy tables for structures viewed in PyMOL. Further, it allows the user to view the energy tables in a 2D plot with energy values represented by a color gradient. This helps to pick out areas of particularly good or bad interaction within a protein. A histogram plot is also available to bin interaction energies.
Publications
Core Repacks (2006)
As a simple test of the EGAD Library source code, we have repacked the cores of three globular proteins: Protein G beta-1 domain, Protein L beta-1 domain, and Ubiquitin. The source code and input files used to perform this calculation are provided as:
Interface Mutants (2006)
This code was used to repack the protein-protein interfaces and predict the effects of mutations on stability, as featured in the EGAD Library paper.
Random Sequence Structure (2002)
The original EGAD used a "random sequence structure" energy to approximate the energy of a residue in the unfolded state of a protein. This calculation can be reproduced using EGAD Library (and a healthy dose of python scripting). The scripts provided below can also be used to generate more standard tripeptide reference energies by reducing the length of the random fragments to 3 residues:
Contributions
Have code that you'd like to have on this page? Contact the egad_lib mailing list!