TY - JOUR
T1 - Analysis of surface structures of hydrogen bonding in protein-ligand interactions using the alpha shape model
AU - Zhou, Weiqiang
AU - Yan, Hong
AU - Hao, Quan
N1 - Funding Information:
This work is supported by the Hong Kong Research Grant Council (Project CityU 123809 ).
Copyright:
Copyright 2012 Elsevier B.V., All rights reserved.
PY - 2012/8/30
Y1 - 2012/8/30
N2 - 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.
AB - 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.
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U2 - 10.1016/j.cplett.2012.07.016
DO - 10.1016/j.cplett.2012.07.016
M3 - Article
AN - SCOPUS:84865544265
SN - 0009-2614
VL - 545
SP - 125
EP - 131
JO - Chemical Physics Letters
JF - Chemical Physics Letters
ER -