free open-source software for automated protein design

Posted by: Anonymous on 05/03/2007 - 04:27 PM

EGAD is a free open-source program for protein design and mutant prediction. EGAD's main focus is performing protein design on fixed backbone scaffolds. 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 and conformational switching, predicting the pK's of ionizable groups in proteins, and generating tables to display the distribution of energetic interactions in protein structures.

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