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SMART: A solvent-accessible triangulated surface generator for molecular graphics and boundary element applications

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Summary

An algorithm is presented for generating a representation of the solvent-accessible molecular surface as a smooth triangulated manifold. The algorithm, called SMART (SMooth moleculAR surface Triangulator), divides the contact and reentrant portions of the solvent-accessible molecular surface into curvilinear three-sided elements. In contrast to the author's earlier implementation of this general approach [Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 11 (1990) 603], the SMART algorithm defines elements directly on the appropriate geometric surface types (rather than using interpolation over cubic elements), and has special features to handle highly distorted regions which often appear in deep crevices and internal cavities. While the method is designed for use with boundary element techniques in continuum electrostatics, it can also be applied to the accurate computation of molecular surface areas and volumes, and the generation of shaded surfaces for display with interactive computer graphics.

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References

  1. Lee, B. and Richards, F.M., J. Mol. Biol., 55 (1971) 379.

    Google Scholar 

  2. Richards, F.M., Annu. Rev. Biophys. Bioeng., 6 (1977) 151.

    Google Scholar 

  3. Wodak, S.J. and Janin, J., Proc. Natl. Acad. Sci. USA, 77 (1980) 1736.

    Google Scholar 

  4. Miertus, S., Scrocco, E. and Tomasi, J., J., Chem. Phys., 55 (1981) 117.

    Google Scholar 

  5. Connolly, M.L., J. Appl. Crystallogr., 18 (1983) 548.

    Google Scholar 

  6. Connolly, M.L., J. Appl. Crystallogr., 18 (1985) 499.

    Google Scholar 

  7. Zauhar, R.J. and Morgan, R.S., J. Mol. Biol., 186 (1985) 815.

    Google Scholar 

  8. Gibson, K.D. and Scheraga, H.A., Mol. Phys., 62 (1987) 1247.

    Google Scholar 

  9. Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 9 (1988) 171.

    Google Scholar 

  10. Meyer, A.Y., J. Comput. Chem., 9 (1988) 18.

    Google Scholar 

  11. Hasel, W., Hendrickson, T.F. and Still, W.C., Tetrahedron Comput. Methodol., 1 (1988) 103.

    Google Scholar 

  12. Higo, J. and Go, N., J. Comput. Chem., 10 (1989) 376.

    Google Scholar 

  13. Karfunkel, H.R. and Eyraud, V., J. Comput. Chem., 10 (1989) 628.

    Google Scholar 

  14. Pascual-Ahuir, J.L. and Silla, E., J. Comput. Chem., 11 (1990) 1047.

    Google Scholar 

  15. Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 11 (1990) 603.

    Google Scholar 

  16. Klein, T.E., Huang, C.C., Pettersen, E.F., Couch, G.S., Ferrin, T.E. and Langridge, R., J. Mol. Graph., 8 (1990) 16.

    Google Scholar 

  17. Heiden, W., Schlenkrich, M. and Brickmann, J., J. Comput.-Aided Mol. Design, 4 (1990) 255.

    Google Scholar 

  18. Perrot, G. and Maigret, B., J. Mol. Graph., 8 (1990) 141.

    Google Scholar 

  19. Silla, E., Tunon, I. and Pascual-Ahuir, J.L., J. Comput. Chem., 12 (1991) 1077.

    Google Scholar 

  20. Kundrot, C.E., Ponder, J.W. and Richards, F.M., J. Comput. Chem., 12 (1991) 402.

    Google Scholar 

  21. Dodd, L.R. and Theodorou, D., Mol. Phys., 72 (1991) 1313.

    Google Scholar 

  22. Wang, H. and Levinthal, C., J. Comput. Chem., 12 (1991) 868.

    Google Scholar 

  23. Heiden, W., Goetze, T. and Brickmann, J., J. Comput. Chem., 14 (1993) 246.

    Google Scholar 

  24. Yoon, B.J. and Lenhoff, A.M., J. Comput. Chem., 11 (1990) 1080.

    Google Scholar 

  25. Juffer, A.H., Botta, E.F.F., Van Keulen, B.A.M., Van der Ploeg, A. and Berendsen, J.C., J. Comput. Phys., 97 (1991) 144.

    Google Scholar 

  26. Connolly, M.L., QCPE Program No. 429, Quantum Chemistry Program Exchange, University of Indiana, Bloomington, IN.

  27. Brocker, Th. and Janich, K., Introduction to Differential Topology, 1st ed., Cambridge University Press, Cambridge, 1982, p. 63.

    Google Scholar 

  28. Protein Data Bank entry 4CLN: Taylor, D.A., Sack, J.S., Maune, J.F., Beckingham, K. and Quiocho, F.A., J. Biol. Chem., 266 (1991) 21375.

    Google Scholar 

  29. Protein Data Bank entry 1ACE: Sussman, J.L., Harel, M. and Silman, I., Science, 253 (1991) 872.

    Google Scholar 

  30. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.

    Google Scholar 

  31. Akin, J.E., Application and Implementation of Finite Element Methods, Academic Press, London, 1982.

    Google Scholar 

  32. Eisenberg, D. and McLachlan, A.D., Nature, 319 (1986) 199.

    Google Scholar 

  33. Ooi, T., Oobatake, M., Nemethy, G. and Scheraga, H., Proc. Natl. Acad. Sci. USA, 84 (1987) 3086.

    Google Scholar 

  34. Hermann, R.B., J. Comput. Chem., 14 (1993) 741.

    Google Scholar 

  35. Varshney, A., BrooksJr., F.P. and Wright, W.V., IEEE Comput. Graph. Appl., 14 (1994) 19.

    Google Scholar 

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Additional information

Availability: Programs (in C) for surface generation, area and volume computation are available from the author. Also available is a graphics display program which runs on Silicon Graphics workstations.

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Zauhar, R.J. SMART: A solvent-accessible triangulated surface generator for molecular graphics and boundary element applications. J Computer-Aided Mol Des 9, 149–159 (1995). https://doi.org/10.1007/BF00124405

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  • DOI: https://doi.org/10.1007/BF00124405

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