Iterative Protein Redesign and Optimization. IPRO redesigns proteins to increase or give specificity to native or novel substrates and cofactors. This is done by repeatedly randomly perturbing the backbones of the proteins around specified design positions, identifying the lowest energy combination of rotamers, and determining if the new design has a lower binding energy than previous ones. The iterative nature of this process allows IPRO to make additive mutations to the protein sequence that collectively improve the specificity towards the desired substrates and/or cofactors. Experimental testing of predictions by IPRO successfully switched the cofactor preference of Candida boidinii xylose reductase from NADPH to NADH.
EGAD: A Genetic Algorithm for protein Design. A free, open-source software package for protein design and prediction of mutation effects on protein folding stabilities and binding affinities. EGAD 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. EGAD can be used with single or multiple processors.
RosettaDesign. A software package, under active development and free for academic use, that has seen extensive successful use. RosettaDesign is accessible via a web server.
SHARPEN. A permissive open-source library for protein design and structure prediction. SHARPEN offers a variety of combinatorial optimization methods (e.g. Monte Carlo, Simulated Annealing, FASTER) and can score proteins using the successful Rosetta all-atom force field or molecular mechanics force fields (OPLSaa). In addition to the protein modeling library, SHARPEN includes tools for scalable distributed computing.
WHAT IF software for protein modelling, design, validation, and visualisation.
CheShift software for protein structure validation.
Abalone software for protein modelling and visualisation.
PROTDES software for protein design based on CHARMM molecular mechanics package.
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