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Methods Enzymol. 2016;578:169-212. doi: 10.1016/bs.mie.2016.05.031. Epub 2016 Jun 25.

Simulation Studies of Protein and Small Molecule Interactions and Reaction.

Author information

1
College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, PR China; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, PR China.
2
College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, PR China; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, PR China. Electronic address: gaoyq@pku.edu.cn.

Abstract

Computational studies of protein and small molecule (protein-ligand/enzyme-substrate) interactions become more and more important in biological science and drug discovery. Computer modeling can provide molecular details of the processes such as conformational change, binding, and transportation of small molecules/proteins, which are not easily to be captured in experiments. In this chapter, we discussed simulation studies of both protein and small molecules from three aspects: conformation sampling, transportations of small molecules in enzymes, and enzymatic reactions involving small molecules. Both methodology developments and examples of simulation studies in this field were presented.

KEYWORDS:

Conformational change; Enhanced sampling; Enzymatic reaction; Ligand binding; Ligand transportation; Molecular simulation

PMID:
27497167
DOI:
10.1016/bs.mie.2016.05.031
[Indexed for MEDLINE]

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