Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy.

ABSTRACT: Interactions between proteins and other molecules play essential roles in all biological processes. Although it is widely held that a protein's ligand specificity is determined primarily by its three-dimensional structure, the general principles by which structure determines ligand binding remain poorly understood. Here we use statistical analyses of a large number of protein-ligand complexes with associated binding-affinity measurements to quantitatively characterize how combinations of atomic interactions contribute to ligand affinity. We find that there are significant differences in how atomic interactions determine ligand affinity for proteins that bind small chemical ligands, those that bind DNA/RNA and those that interact with other proteins. Although protein-small molecule and prot

SUBMITTER: Dias R 

PROVIDER: S-EPMC5054890 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature