After selecting your drug/ligand & DNA/receptor; you can do CHIMERA of your DNA (for removal of water molecule, etc.) and then you can use AutoDock for docking your ligand to the receptor by selecting the appropriate methods and parameters.
following is the link to AutoDock tutorial that might help you:
http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf
Hi Ako, firstly identity the precise drug target (based on molecular cause of disease), modeling and validate it using resources and biotools. Then identity its binding site(structure based drug discovery and development) using CastP. Then u can design lead molecule or it can be imported from small chemical database is pubchem,chemspider validate it. Then go for molecular docking. For docking u can use swissdock, discovery studio,hex.
After selecting your drug/ligand & DNA/receptor; you can do CHIMERA of your DNA (for removal of water molecule, etc.) and then you can use AutoDock for docking your ligand to the receptor by selecting the appropriate methods and parameters.
following is the link to AutoDock tutorial that might help you:
http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf
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