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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 querystructures for conserved 3D motifs. Applications of templates are discussed, aswell as some exemplar cases for examining evolutionary links in enzymes. Wealso introduce the concept of using more than one template per structure torepresent flexible sites, as an approach to better understand catalysis throughsnapshots captured in enzyme structures. Functional annotation from structureis an important topic that has recently resurfaced due to the new more accuratemethods of protein structure prediction. Therefore, we anticipate thattemplate-based functional site detection will be a powerful tool in the task ofcharacterising a vast number of new protein models.

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