Molecular docking

molecular docking
Regards,
SHRIHITH.A
MSc Microbiology,
Department of Microbiology & Biotechnology,
Bangalore University

1. MOLECULAR DOCKING PRESENTED BY, SHRIHITH.A

2. A molecule is the smallest particle in a chemical element or compound that has the chemical properties of that element or compound . A Molecules are made up of atoms that are held together by chemical bonds. These bonds form as a result of the sharing or exchange of electron s among atoms. MOLECULES

3. Docking attempts to find the “best” matching between two molecules. Docking is the computational determination of binding affinity between molecules (protein structure and ligand). DOCKING

4. Molecular docking tries to predict the structure of the intermolecular complex formed between two or more constituent molecules. Molecular docking has become an increasingly important tool for drug discovery. DEFENITION

5. It is of extreme relevance in cellular biology , where function is accomplished by proteins interacting with themselves and with other molecular components It is the key to rational drug design : The results of docking can be used to find inhibitors for specific target proteins and thus to design new drugs. It is gaining importance as the number of proteins whose structure is known increases Why docking is important?

6. Protein-Protein Docking Both molecules usually considered rigid. 6 degrees of freedom First apply steric constraints to limit search space and the examine energetics of possible binding conformations Types of docking

7. Protein-Ligand Docking Flexible ligand, rigid-receptor Search space much larger Either reduce flexible ligand to rigid fragments connected by one or several hinges, or search the conformational space using monte-carlo methods or molecular dynamics CONT…

8. IN- silico generation of ligands(using chemsketch in this software we can draw the structure of Ligand/molecule). Conversion of file format( O PEN BABEL is the software used to converting format of file . mol to . pdb STEPS FOLLOWED FOR MOLECULAR DOCKING

9. Protein optimization(RCSB- protein data bank, here you can prepare your protein of interest for docking).www.rcsb.org Energy Minimization( here SPDV swiss-Pdb viewer software) Tis can be done by commanding.

10. Molecular docking (creation of . gpf -grid parameter file and . dpf -dock parameter file 1) Autodock Vina 2) Autodock 4.0 3) Autodock 4.2 This are the software used to make auto griding and dock parameters along with grid mapping

11. Running the docking algorithm(CYGWIN-1 in this software we will create GLG file and DLG file here this software works commanding after getting succesfull comand for auto grid( glg ) and auto dock ( dlg ) After this step we got to know minimal binding energy CYGWIN-2

12. Hydrogen bond analysis( UCSF CHIMERA we use this software for visulisation and analysis of result ADMET( the molecules which have shown H-bond with the active site residue or any other residue of the binding pocket note down those molecules and then run these molecule on the online ADMET servers

13. molecular properties http://molsoft.com/mprop/ Toxicity and bioactivity http://organic-chemistry.org/prog/peo/ ADMET studies https://ilab.acdlabs.com/iLab2/ CONT…

14. Structure based drug design Lead Optimization Virtual Screening Protein-Protein Docking Chemical mechanism studies. APPLICATIONS