The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.

ABSTRACT: Accurate potential energy models are necessary for reliable atomistic simulations of chemical phenomena. In the realm of biomolecular modeling, large systems like proteins comprise very many noncovalent interactions (NCIs) that can contribute to the protein's stability and structure. This work presents two high-quality chemical databases of common fragment interactions in biomolecular systems as extracted from high-resolution Protein DataBank crystal structures: 3380 sidechain-sidechain interactions and 100 backbone-backbone interactions that inaugurate the BioFragment Database (BFDb). Absolute interaction energies are generated with a computationally tractable explicitly correlated coupled cluster with perturbative triples [CCSD(T)-F12] "silver standard" (0.05 kcal/mol average error) for

SUBMITTER: Burns LA 

PROVIDER: S-EPMC5656042 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature