Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program.

ABSTRACT: We have developed a set of protocols in the molecular modeling program Rosetta for performing requirement-driven protein design. First, the user specifies a set of structural features that need to be present in the designed protein. These requirements can be general (e.g., "create a protein with five helices"), or they can be very specific and require the correct placement of a set of amino acids to bind a ligand. Next, a large set of protein models are generated that satisfy the design requirements. The models are built using a method that we recently introduced into Rosetta, called SEWING, that rapidly assembles novel protein backbones by combining pieces of naturally occurring proteins. In the last step of the process, rotamer-based sequence optimization and backbone refinement are perf

SUBMITTER: Guffy SL 

PROVIDER: S-EPMC5975180 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature