Nashrieh Shimi va Mohandesi Shimi Iran

Nashrieh Shimi va Mohandesi Shimi Iran

Application of semi-empirical quantum mechanical methods in estimation of biomolecular interactions

Document Type : Review Article

Authors
Mohammad Hossein Karimi-Jafari 1
Rohoullah Firouzi 2
Saleh Bagheri 2
1 Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
2 Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
Abstract
Despite considerable progress in computational methods for calculating interactions between small molecules and proteins, estimation of the geometry of protein-ligand complexes and their binding free energies remains as a challenging task in the structure-based drug design. For an accurate description of these interactions requires the inclusion of quantum mechanical contributions using an extended atomic orbital basis set. For this purpose, some semi-empirical quantum mechanical methods have been developed that are much less expensive than more accurate “ab initio” and “density functional theory” methods.Currently, the application of fast and efficient semi-empirical quantum mechanical methods for calculating electronic properties of large molecules and biological systems becomes a routine task. In this contribution, the development of these methods and their successful applications in different fields – especially in biomolecular interactions – are reviewed.
Keywords
Semi-empirical quantum mechanical methods
Non-covalent interactions
Drug design
Biomolecules

Subjects

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