Dataset Information

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 NCI that demands only a fraction of the cost of the conventional "gold standard," CCSD(T) at the complete basis set limit. By sampling extensively from biological environments, BFDb spans the natural diversity of protein NCI motifs and orientations. In addition to supplying a thorough assessment for lower scaling force-field (2), semi-empirical (3), density functional (244), and wavefunction (45) methods (comprising >1M interaction energies), BFDb provides interactive tools for running and manipulating the resulting large datasets and offers a valuable resource for potential energy model development and validation.

SUBMITTER: Burns LA

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

REPOSITORIES: biostudies-literature

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

Burns Lori A LA Faver John C JC Zheng Zheng Z Marshall Michael S MS Smith Daniel G A DGA Vanommeslaeghe Kenno K MacKerell Alexander D AD Merz Kenneth M KM Sherrill C David CD

The Journal of chemical physics 20171001 16

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 interact ...[more]

PMID: 29096505

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Dataset Information

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

Publications

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

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