OSPREY (Open Source Protein REdesign for You)is a suite of programs for computational structure-based protein design.OSPREY is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.). OSPREY can also be used for predicting small-molecule inhibitors. With certain limitations, the current version of OSPREY can also model protein-protein and protein-peptide interactions.
gOSPREY is the abbreviation for Open Source Protein REdesign for You on a GPU. It enables the user to utilize a GPU to accelerate the procedure of protein design in a massive parallel fashion.
EvoDesign is an evolutionary profile based approach to de novo protein design. Starting from a scaffold of target protein structure, EvoDesign first identifies protein families which have similar fold from the PDB library by TM-align. A structural profile is then constructed from the protein templates which is used to guide the conformation search of amino acid sequence space, where physicochemical packing is accommodated by the single-sequence based solvation, torsion angle and secondary structure predictions. The final designed sequence is obtained by clustering all sequence decoys generated during design simulations.
