A mathematical representation of protein binding sites using structural dispersion of atoms from principal axes for classification of binding ligands.

ABSTRACT: Many researchers have studied the relationship between the biological functions of proteins and the structures of both their overall backbones of amino acids and their binding sites. A large amount of the work has focused on summarizing structural features of binding sites as scalar quantities, which can result in a great deal of information loss since the structures are three-dimensional. Additionally, a common way of comparing binding sites is via aligning their atoms, which is a computationally intensive procedure that substantially limits the types of analysis and modeling that can be done. In this work, we develop a novel encoding of binding sites as covariance matrices of the distances of atoms to the principal axes of the structures. This representation is invariant to the chosen co

SUBMITTER: Premarathna GI 

PROVIDER: S-EPMC8031081 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature