Ligand docking and binding site analysis with pymol and autodock/vina

  • Abstract
  • Keywords
  • References
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  • Abstract

    Docking of various therapeutically important chemical entities to the specific target sites offers a meaningful strategy that may have tremendous scope in a drug design process. For a thorough understanding of the structural features that determine the strength of bonding between a ligand with its receptor, an insight to visualize binding geometries and interaction is mandatory. Bioinformatical as well as graphical software ‘PyMOL’ in combination with the molecular docking suites Autodock and Vina allows the study of molecular combination to visualize and understand the structure-based drug design efforts. In the present study, we outlined a user friendly method to perform molecular docking using vina and finally the results were analyzed in pymol in both two as well as three-dimensional orientation. The operation bypasses the steps that are involved in docking using cygwin terminal like formation of gpf and dpf files. The simple and straight-forward operation method does not require formal bioinformatics training to apprehend molecular docking studies using AutoDock 4.2 program.

  • Keywords

    Auto-Dock; Chemdraw; DSV (Discovery Studio Visualizer); PDB (Protein Data Bank) and Pubchem: PYMOL.

  • References

      [1] Muegge I and Rarey M. Reviews in Computational Chemistry. John Wiley & Sons, Inc., (2001), pp 1-60.

      [2] Holloway KM et al., A priori prediction of HIV I protease inhibitors employing energy minimization in the active site. J Med Chem Vol 38 (1995), pp 305-317.

      [3] Vieth M, Cummins DJ. DoMCoSAR: a novel approach for establishing the docking mode that is consistent with the structure-activity relationship. Application to HIV-1 protease inhibitors and VEGF receptor tyrosine kinase inhibitors. J Med Chem. Vol.43, No.16, (2000), pp 3020-3032.

      [4] Gilbert D. Bioinformatics software resources. Brief Bioinform. Volume 3, (2004), pp 300-304. Review

      [5] Lazarova M. Virtual screening models, methods and software systems. International Scientific Conference Computer Science, (2008), pp 55-60.




Article ID: 4123
DOI: 10.14419/ijbas.v4i2.4123

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