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Journal of Chemistry
Volume 2013, Article ID 803151, 6 pages
http://dx.doi.org/10.1155/2013/803151
Research Article

ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server

1Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rua Marquês de São Vicente 225, Gávea, 22453-900 Rio de Janeiro, RJ, Brazil
2Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Praça General Tibúrcio, 80, Urca, 22290-270 Rio de Janeiro, RJ, Brazil

Received 30 June 2012; Accepted 3 August 2012

Academic Editor: Cristiano R. W. Guimarães

Copyright © 2013 Diogo de Jesus Medeiros et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation,” Journal of Chemical Theory and Computation, vol. 4, no. 3, pp. 435–447, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. Q. Wang, N. H. Werstiuk, J. R. Kramer, and R. A. Bell, “Effects of Cu ions and explicit water molecules on the copper binding domain of amyloid precursor protein APP(131-189): a molecular dynamics study,” Journal of Physical Chemistry B, vol. 115, no. 29, pp. 9224–9235, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. K. Ohno, T. Mitsui, Y. Tanida et al., “Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors,” Journal of Molecular Modeling, vol. 17, no. 2, pp. 383–389, 2011. View at Publisher · View at Google Scholar · View at Scopus
  4. A. Hung and I. Yarovsky, “Inhibition of peptide aggregation by lipids: insights from coarse-grained molecular simulations,” Journal of Molecular Graphics and Modelling, vol. 29, no. 5, pp. 597–607, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. P. Lazar, S. Kim, Y. Lee, and K. W. Lee, “Computational approach to ensure the stability of the favorable ATP binding site in E. coli Hfq,” Journal of Molecular Graphics and Modelling, vol. 29, no. 4, pp. 573–580, 2010. View at Publisher · View at Google Scholar · View at Scopus
  6. P. Lazar, Y. Lee, S. Kim, M. Chandrasekaran, and K. W. Lee, “Molecular dynamics simulation study for ionic strength dependence of RNA-host factor interaction in Staphylococcus aureus Hfq,” Bulletin of the Korean Chemical Society, vol. 31, no. 16, pp. 1519–1526, 2010. View at Publisher · View at Google Scholar · View at Scopus
  7. S. J. Irudayam and M. L. Berkowitz, “Influence of the arrangement and secondary structure of melittin peptides on the formation and stability of toroidal pores,” Biochimica et Biophysica Acta, vol. 1808, no. 9, pp. 2258–2266, 2011. View at Publisher · View at Google Scholar · View at Scopus
  8. R. P. Wesołowski, S. Furmaniak, A. P. Terzyk, and P. A. Gauden, “Simulating the effect of carbon nanotube curvature on adsorption of polycyclic aromatic hydrocarbons,” Adsorption, vol. 17, no. 1, pp. 1–4, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. A. J. Beevers and A. Kukol, “Conformational flexibility of the peptide hormone ghrelin in solution and lipid membrane bound: a molecular dynamics study,” Journal of Biomolecular Structure and Dynamics, vol. 23, no. 4, pp. 357–364, 2006. View at Google Scholar · View at Scopus
  10. P. Narang, K. Bhushan, S. Bose, and B. Jayaram, “Protein structure evaluation using an all-atom energy based empirical scoring function,” Journal of Biomolecular Structure and Dynamics, vol. 23, no. 4, pp. 385–406, 2006. View at Google Scholar · View at Scopus
  11. Y. Tao, Z. H. Rao, and S. Q. Liu, “Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K,” Journal of Biomolecular Structure and Dynamics, vol. 28, no. 2, pp. 143–157, 2010. View at Google Scholar · View at Scopus
  12. A. W. Schüttelkopf and D. M. F. van Aalten, “PRODRG: a tool for high-throughput crystallography of protein-ligand complexes,” Acta Crystallographica D, vol. 60, no. 8, pp. 1355–1363, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. W. L. Jorgensen and J. Tirado-Rives, “The OPLS potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin,” Journal of the American Chemical Society, vol. 110, no. 6, pp. 1657–1666, 1988. View at Google Scholar · View at Scopus
  14. W. F. van Gunsteren, S. R. Billeter, A. A. Eising et al., “Biomolecular simulation,” in The GROMOS96 Manual and User Guide, vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v., Groningen, The Netherlands, 1996. View at Google Scholar
  15. W. D. Cornell, P. Cieplak, C. I. Bayly et al., “A second generation force field for the simulation of proteins, nucleic acids, and organic molecules,” Journal of the American Chemical Society, vol. 117, no. 19, pp. 5179–5197, 1995. View at Publisher · View at Google Scholar · View at Scopus
  16. S. J. Weiner, P. A. Kollman, D. A. Case et al., “A new force field for molecular mechanical simulation of nucleic acids and proteins,” Journal of the American Chemical Society, vol. 106, no. 3, pp. 765–784, 1984. View at Google Scholar · View at Scopus
  17. W. A. Cortopassi, A. A. Oliveira, A. P. Guimarães, M. N. Rennó, A. U. Krettli, and T. C. C. França, “Docking studies on the binding of quinoline derivatives and hematin to Plasmodium falciparum lactate dehydrogenase,” Journal of Biomolecular Structure and Dynamics, vol. 29, no. 1, pp. 207–218, 2011. View at Google Scholar · View at Scopus
  18. J. Penna-Coutinho, W. A. Cortopassi, A. A. Oliveira, T. C. C. França, and A. U. Krettli, “Antimalarial activity of potential inhibitors of Plasmodium falciparum lactate dehydrogenase enzyme selected by docking studies,” PLoS ONE, vol. 6, no. 7, Article ID e21237, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. S. S. Tatke, V. Renugopalakrishnan, and M. Prabhakaran, “Interfacing biological macromolecules with carbon nanotubes and silicon surfaces: a computer modelling and dynamic simulation study,” Nanotechnology, vol. 15, no. 10, pp. S684–S690, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. A. W. Schüttelkopf, O. A. Andersen, F. V. Rao et al., “Screening-based discovery and structural dissection of a novel family 18 chitinase inhibitor,” The Journal of Biological Chemistry, vol. 281, no. 37, pp. 27278–27285, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Subashini, P. V. Devarajan, G. S. Sonavane, and M. Doble, “Molecular dynamics simulation of drug uptake by polymer,” Journal of Molecular Modeling, vol. 17, no. 5, pp. 1141–1147, 2011. View at Publisher · View at Google Scholar · View at Scopus
  22. A. P. Guimarães, A. A. Oliveira, E. F. F. Da Cunha, T. C. Ramalho, and T. C. C. França, “Design of new chemotherapeutics against the deadly anthrax disease. Docking and molecular dynamics studies of inhibitors containing pyrrolidine and riboamidrazone rings on nucleoside hydrolase from Bacillus anthracis,” Journal of Biomolecular Structure and Dynamics, vol. 28, no. 4, pp. 455–469, 2011. View at Google Scholar · View at Scopus
  23. A. A. Oliveira, M. N. Rennó, C. A. S. Matos et al., “Molecular modeling studies of yersinia pestis dihydrofolate reductase,” Journal of Biomolecular Structure and Dynamics, vol. 29, no. 2, pp. 351–367, 2011. View at Google Scholar
  24. D. T. Mancini, K. S. Matos, E. F. F. Cunha et al., “Molecular modeling studies on nucleoside hydrolase from the biological warfare agent Brucella suis,” Journal of Biomolecular Structure & Dynamics, vol. 30, pp. 125–136, 2012. View at Google Scholar
  25. A. P. Guimarães, A. A. Oliveira, E. F. F. da Cunha, T. C. Ramalho, and T. C. C. França, “Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation,” Journal of Molecular Modeling, vol. 17, pp. 2939–2951, 2011. View at Publisher · View at Google Scholar · View at Scopus
  26. J. A. Lemkul, W. J. Allen, and D. R. Bevan, “Practical considerations for building GROMOS-compatible small-molecule topologies,” Journal of Chemical Information and Modeling, vol. 50, no. 12, pp. 2221–2235, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. M. W. Schmidt, K. K. Baldridge, J. A. Boatz et al., “General atomic and molecular electronic structure system,” Journal of Computational Chemistry, vol. 14, no. 11, pp. 1347–1363, 1993. View at Google Scholar
  28. M. Valiev, E. J. Bylaska, N. Govind et al., “NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations,” Computer Physics Communications, vol. 181, no. 9, pp. 1477–1489, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. J. P. Stewart, “MOPAC, 2009,” James Stewart Computational Chemistry, Colorado Springs, CO, USA, 2008, http://OpenMOPAC.net.
  30. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., Gaussian03 03, Revision C.02, Gaussian03, Inc., Wallingford CT, 2004.
  31. A. S. Christensen, S. P. A. Sauer, and J. H. Jensen, “Definitive benchmark study of ring current effects on amide proton chemical shifts,” Journal of Chemical Theory and Computation, vol. 7, no. 7, pp. 2078–2084, 2011. View at Publisher · View at Google Scholar · View at Scopus
  32. V. W. Day, M. A. Hossain, O. K. Sung, D. Powell, G. Lushington, and K. Bowman-James, “Encircled proton,” Journal of the American Chemical Society, vol. 129, no. 28, pp. 8692–8693, 2007. View at Publisher · View at Google Scholar · View at Scopus
  33. L. M. Goldman, D. R. Glowacki, and B. K. Carpenter, “Nonstatistical dynamics in unlikely places: [1,5] Hydrogen migration in chemically activated cyclopentadiene,” Journal of the American Chemical Society, vol. 133, no. 14, pp. 5312–5318, 2011. View at Publisher · View at Google Scholar · View at Scopus