Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta.

ABSTRACT: Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the r

SUBMITTER: Combs SA 

PROVIDER: S-EPMC6755676 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature