An efficient algorithm for multistate protein design based on FASTER

By Benjamin D. Allen, Stephen L. Mayo. 2009

55 citations recorded by the source corpus.

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Algorithms for Protein Design (2016, methodology): “Allen and Mayo [81] adapted the FASTER algorithm, a heuristic optimization algorithm developed for protein design, to the multistate case.”
Recent advances in de novo protein design: Principles, methods, and applications (2021, methodology): “Side chains were then designed by optimizing the Boltzmann-weighted average energy of all members from the ensemble using the fast and accurate side chain topology and energy refinement algorithm (153).”
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences (2015, methodology): “Additional rotamer optimization algorithms have been adapted for use in MSD, such as dead-end elimination [36], probabilistic graphical models [37], and iterative batch relaxation/single perturbation and relaxation [35].”
A Generic Program for Multistate Protein Design (2011, methodology): “, the implementation is suited to perform both positive and negative design. We have tuned the parameters of our genetic algorithm to behave as well as Rosetta's existing single-state design algorithm at single-state design problems, but we have not compared the genetic algorithm's performance to th”