Workshop 2:
Theoretical Chemistry Tools ‘Gaussian03’ Software Towards Molecular Docking
Pr. Meziane Brahimi (USTHB - Alger)
Laboratoire de Physico Chimie Théorique
et Chimie Informatique (LPCTCI), Faculté de Chimie. USTHB
Mail: mez_brahimi@yahoo.fr
Mobile: 0 659 678 439
Abstract
This course aims to give an overview of the use of theoretical chemistry methods (quantum and classical) in the preparation of a molecular docking protocol. For this purpose, we will use Gaussian03 and GaussView software for the optimization of ligands at density functional theory (DFT) levels. The results files will be converted into a file with the PDB extension usable by molecular docking software including Chimera 1.14 which will be used because of its simplicity.
In application, we will use the PDB 6LZG file representing the contact interface between the Spike protein of SARS-COV2 and the human target protein ACE2 with various ligands taken from the literature.
Outline
I- Presentation of Gaussian 03W and GaussView software for the optimization of ligands at the DFT level. (Based on 2h)
a. Presentation of software and common keywords used.
b. Use of data files according to:
- the Z-Matrix or the coordinates of the molecule to be studied
- use of GaussView
c. Exploitation of results.
d. transfer of the results file with .log or .out extension to a PDB file using GaussView.
e. Opening of the PDB file by Chimera 1.14.
II- Presentation and use of molecular docking software Chimera 1.14. (Based on 2h)
a. Use of "PDB" databases for the research of targets used in molecular docking.
b. Preparation of targets and ligands
c. Choosing the best docking site
d. Launch of the docking calculation
e. Exploitation of the results.
III. Workshop. (Based on 3h)
The 6LGZ PDB file, which models the interaction surface between the spike-protein of SARS-COV2 and the human ACE2 receptor protein, will be taken as an example.
