Paper Titles in Periodical
International Letters of Natural Sciences
ILNS Volume 16

Subscribe to our Newsletter and get informed about new publication regulary and special discounts for subscribers!

ILNS > ILNS Volume 16 > Docking for Drug Interface Residues of Modelled...
< Back to Volume

Docking for Drug Interface Residues of Modelled VPS33B of Human with PtpA of Mycobacterium tuberculosis CDC1551

Full Text PDF


VPS33B, a human Vacuolar Protein Sorting (VPS) protein which mediates the phagolysosomal fusion in macrophage of the eukaryotic organisms. This protein has a great role during the mycobacterial infections, which binds with the Mycobacterium protein tyrosine phosphatase A (PtpA). A single functional domain of PtpA has been identified using SMART domain databases, followed by finding the antigenicity of PtpA using CLC main workbench tool. The protein-protein interaction network predicts the interface of biological functions of proteins, built by using Cytoscape 2.8.3 version tool for manual literature survey of protein sets. According to the literature the specific interactivity of PtpA with VPS33B of human lead to pathogenesis, and provided a good platform to find the structure of VPS33B as it lacks the 3 dimensional structure in PDB. Homology Modelling of VPS33B provides a significant properties to design a specific drug through screening the drug databases (eDrug3D). The modelled protein has been validated through SAVES server maintained by NIH and UCLA with the standard Ramachandran plot with accuracy of 90.7 %. From our findings the interface residues are very crucial points which has been found through docking the modelled protein and Mycobacterium protein and interface residues were selected manually using PyMol software


International Letters of Natural Sciences (Volume 16)
K. M. Reddy et al., "Docking for Drug Interface Residues of Modelled VPS33B of Human with PtpA of Mycobacterium tuberculosis CDC1551", International Letters of Natural Sciences, Vol. 16, pp. 179-196, 2014
Online since:
May 2014

Ge H., Walhout A.J., Vidal M., Trends Genetics 19 (2003) 551-560.

Hong Yu, 2007. Ph. D dissertation, A&M University. Texas.

R. D. Fleischmann, D. Alland, J. A. Eisen et al., Journal of Bacteriology 184 (2002) 5479-5490.

Reddy T. B. K., Robert Riley K. Schoolnik Gary, Nucleic Acids Research 37 (2009) D499-D508.

Dennis Wong, D. Joseph Chao, Yossef Av-Gay, Trends in Microbial Biotechnology 21 (2013) 100-109.

Manuela Pruess, Paul Kersey, Rolf Apweiler, Insilico biology 5 (2004) 0017.

CLC bio A/S. The CLC Main Workbench 6. 8 is developed by Science Park Aarhus. Finlandsgade, 8200 Aarhus N, and Denmark. (2013) 10-12.

A. S. Kolaskar, P. C. Tongaonkar, FEBS Letters 276 (1990) 172-174.

E. E. Snyder, N. Kampanya, et al., Nucleic Acids Research 35 (2006) D401-D406.

D. Tim Driscoll, Matthew Dyer, T. M. Murali, et al., Nucleic Acids Research 37 (2009) D647-D650.

Paul Shannon, Andrew Markiel, Owen Ozier, Genome Research 13 (2003) 2498-2504.

Jorg Schultz, Frank Milpetz, Peer Bork, et al., Proceedings of the National Academy of Sciences USA 95 (1998) 5857-5864.

M. Helen Berman, John Westbrook, Zukang Feng, et al., Nucleic Acids Research 28 (2000) 235-242.

R.A. Laskowski, E.G. Hutchinson, A.D. Michie, et al., Trends in Biochemical Sciences 22 (1997) 488-490.

Bhusan K. Kuntal, Polamarasetty Aparoy, Pallu Reddanna, BMC Research Notes 3 (2010) 226.

WL. DeLano, DeLano Scientific, San Carlos, California CCP4 Newsletter on Protein Crystallography (2002).

R. A. Laskowski, M. W. MacArthur, D. S. Moss, et al., Journal of Applied Crystallography 26 (1993) 283-291.

S. F. Altschul, T. L. Madden, A. A. Schäffer, et al., Nucleic Acids Research 25 (1997) 389-402.

S. F. Altschul, W. Gish, W. Miller, et al., Journal of Molecular Biology 215 (1990) 403-410.

S. S. Sheik, P. Sundararajan, Hussain A.S.Z. et al., Bioinformatics 18 (2002) 1548-1549.

Ranjit Kumar, Bindu Nanduri, BMC Bioinformatics 11 (2010) 1471-2105.

T. David Barkan, P. Fred Davis, Narayanan Eswar., et al., Protein Science 16 (2007) 2585-2596.

Paolo Gaibani, T. Maria Pellegrino, Giada Rossini, et al., BMC Infectious Diseases 10 (2010) 1471-2334.

J. Schultz, R. R. Copley, T. Doerks, et al., Nucleic Acids Research 28 (2000) 231-234.

U. Pieper, N. Eswar, H. Braberg, et al., Nucleic Acids Research 34 (2006) D291-D295. ( Received 20 May 2014; accepted 28 May 2014 ).

Show More Hide
Cited By:
This article has no citations.