Capturing the geometry, function, and evolution of enzymes with 3D templates.

ABSTRACT: Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs, or catalytic sites. Here we explore methods to generate template libraries and algorithms to query structures for conserved 3D motifs. Applications of templates are discussed, as well as some exemplar cases for examining evolutionary links in enzymes. We also introduce the concept of using more than one template per structure to represent flexible sites, as an approach to better understand catalysis through snapshots captured in enzyme structures. Functional annotation from structure is an important topic that has recently resurfaced due to the new more accurate methods of protein structure prediction. Therefore, we anticipate that template-based functio

SUBMITTER: Riziotis IG 

PROVIDER: S-EPMC9207746 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature