User's Manual for
EGAD! a Genetic Algorithm for protein Design!
(stand alone program)
EGAD's (Egad! a Genetic Algorithm for protein Design) main focus is
performing protein design on fixed backbone scaffolds. All the major
rotamer-optimization methods such as genetic algorithms (GA), monte
carlo simulated annealing (MC), self-consistent
mean-field optimization
(SCMF), fast and accurate side-chain topology and energy refinement
(FASTER), and dead-end elimination (DEE) have been implemented
in EGAD. It can also consider multiple structures
simultaneously for
designing specific binding proteins or locking proteins into specific
conformational states. In addition to natural protein residues, EGAD
can also consider free-moving ligands with or
without rotatable bonds. It may even be possible to use EGAD for drug design.
EGAD can be used with a single processor, but it can take advantage of
the power of parallelization to perform certain
jobs quickly.
Some of the tasks EGAD can
perform are:
- prediction of mutation effects
on protein
stability and protein-complex formation
to within ~1kcal/mol
- automated scanning mutagenesis, including
saturation mutagenesis, of proteins and protein complexes
- total protein sequence design
- design of ligand binding sites
- optimization of sequences while
considering
multiple structures for
the design of specific binding proteins, conformational switching, etc.
- predicting the pK's of
ionizable groups in proteins
- generating tables to display the
distribution of
energetic interactions in protein structures
- minimizing protein structure
energies by adjusting
dihedral angles
For a more complete discussion of protein design, please see my thesis
and/or these other reviews (Pokala
and Handel 2001; Kortemme
and Baker
2004; Kuhlman and Baker
2004; Ventura and
Serrano 2004; Pokala and
Handel 2005).
This documentation is for the stand-alone EGAD program. Using this
program does not require any programming knowledge.
Table
of Contents
(html) or
download EGAD User's Manual (pdf)
Links:
download the EGAD program
with example files installation instructions
Table of Contents
(html) or download EGAD User's Manual (pdf)
examples/
download
Navin Pokala's
Thesis (pdf)
source_code/
If you use EGAD, please cite:
Pokala N, Handel TM. Energy
functions for protein design: adjustment with protein-protein
complex affinities, models for the unfolded state, and negative design
of solubility & specificity. J Mol Biol. 347(1): 203-227. (2005).
[download pdf]
[medline]
This program is distributed under the GNU public license (http://www.gnu.org/copyleft/gpl.html
and COPYRIGHT_AND_LICENSE). It is provided as
is, with absolutely no warranty expressed or implied.
The EGAD
stand-alone program is no longer under active development.
Nevertheless, I
(Navin Pokala; navin @ annapurna . berkeley . edu) might be able to
help you out, collaborate, and/or give you advice, depending on the
problem. However, starting July 2005, I will be a postdoc studying C elegans
neurobiology at The
Rockefeller University in Cori
Bargmann's lab, so the time I can dedicate may be limited.
Also check out
the EGAD library project,
which is
under active development. This project is aimed primarily at
programmers, although programs and scripts for end-users are available.
You might also consider formally collaborating with the Handel lab.
back to Handel
Lab homepage