A novel approach in molecular docking was successfully used to reproduce protein-ligand experimental geometries. When dealing with halogenated compounds the correct description of halogen bonds between the ligand and the protein is shown to be essential. Applying a simple molecular mechanistic model for halogen bonds improved the protein-ligand geometries as well as halogen bond features, which makes it a promising tool for future computer-aided drug development.

Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center Academy of Sciences of the Czech Republic Flemingovo nam 2 16610 Prague 6 Czech Republic

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Could Quantum Mechanical Properties Be Reflected on Classical Molecular Dynamics? The Case of Halogenated Organic Compounds of Biological Interest