The Use of Chlorobenzene as a Probe Molecule in Molecular Dynamics Simulations

We map ligand binding sites on protein surfaces in molecular dynamics simulations using chlorobenzene as a probe molecule. The method was validated on four proteins. Two types of affinity maps that identified halogen and hydrophobic binding sites on proteins were obtained. Our method could prove use...

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Bibliographic Details
Published inJournal of chemical information and modeling Vol. 54; no. 7; pp. 1821 - 1827
Main Authors Tan, Yaw Sing, Spring, David R, Abell, Chris, Verma, Chandra
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 28.07.2014
Subjects
Binding Sites
Chlorobenzenes - chemistry
Drug Discovery
Ligands
Molecular Dynamics Simulation
Molecular Probes - chemistry
Molecules
Organic chemicals
Protein Conformation
Proteins
Proteins - chemistry
Simulation
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Summary:We map ligand binding sites on protein surfaces in molecular dynamics simulations using chlorobenzene as a probe molecule. The method was validated on four proteins. Two types of affinity maps that identified halogen and hydrophobic binding sites on proteins were obtained. Our method could prove useful for the discovery and development of halogenated inhibitors.
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ISSN:1549-9596
1549-960X
DOI:10.1021/ci500215x