AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design.

ABSTRACT: With advances in protein structure predictions, the number of available high-quality structures has increased dramatically. In light of these advances, structure-based enzyme engineering is expected to become increasingly important for optimizing biocatalysts for industrial processes. Here, we present AsiteDesign, a Monte Carlo-based protocol for structure-based engineering of active sites. AsiteDesign provides a framework for introducing new catalytic residues in a given binding pocket to either create a new catalytic activity or alter the existing one. AsiteDesign is implemented using pyRosetta and incorporates enhanced sampling techniques to efficiently explore the search space. The protocol was tested by designing an alternative catalytic triad in the active site of Pseudomonas fluo

SUBMITTER: Roda S 

PROVIDER: S-EPMC10068746 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature