DiffBond: A Method for Predicting Intermolecular Bond Formation

Tam, Justin; Palumbo, Talulla B.; Miwa, Julie M.; Chen, Brian Y.

doi:10.1109/bibm52615.2021.9669850

Cited by 1 publication

(1 citation statement)

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“…Chemical literature defines salt bridges as the co-occurrence of both a hydrogen bond and an ionic bond; salt bridge measurements must also exist under the same biological assumptions as those of ionic bonds. Following these definitions, we extend upon [ 4 ] to present DiffBond, a method for identifying and classifying intermolecular bonds while applying standard definitions of bonds in chemical literature to explain protein interactions. This paper paraphrases significantly the implementation and verification of DiffBond and also adds additional verification of DiffBond with affinity data.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Protein-Protein Interactions for Intermolecular Bond Prediction

et al. 2022

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Protein-protein interactions often involve a complex system of intermolecular interactions between residues and atoms at the binding site. A comprehensive exploration of these interactions can help reveal key residues involved in protein-protein recognition that are not obvious using other protein analysis techniques. This paper presents and extends DiffBond, a novel method for identifying and classifying intermolecular bonds while applying standard definitions of bonds in chemical literature to explain protein interactions. DiffBond predicted intermolecular bonds from four protein complexes: Barnase-Barstar, Rap1a-raf, SMAD2-SMAD4, and a subset of complexes formed from three-finger toxins and nAChRs. Based on validation through manual literature search and through comparison of two protein complexes from the SKEMPI dataset, DiffBond was able to identify intermolecular ionic bonds and hydrogen bonds with high precision and recall, and identify salt bridges with high precision. DiffBond predictions on bond existence were also strongly correlated with observations of Gibbs free energy change and electrostatic complementarity in mutational experiments. DiffBond can be a powerful tool for predicting and characterizing influential residues in protein-protein interactions, and its predictions can support research in mutational experiments and drug design.

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Section: Introductionmentioning

confidence: 99%