Analysis of surface structures of hydrogen bonding in protein-ligand interactions using the alpha shape model

Weiqiang Zhou, Hong Yan, Quan Hao

Research output: Contribution to journalArticlepeer-review

Abstract

Hydrogen bonding provides useful information for the study of protein-ligand interactions. However, the physical role that a hydrogen bond plays and its 3D surface characteristics in protein-ligand interaction are still not well understood. We apply the 3D alpha shape model to reconstruct the interface of a protein-ligand structure and use solid angles at interface atoms to represent the surface geometric properties of a hydrogen bond. The result shows that 77.2% of the hydrogen bonds show complementary geometric patterns and 95.0% of the protein-ligand complexes contain at least one such hydrogen bond.

Original languageEnglish (US)
Pages (from-to)125-131
Number of pages7
JournalChemical Physics Letters
Volume545
DOIs
StatePublished - Aug 30 2012
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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