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A Fast Method for Determination of Solvent-Exposed Atoms and Its Possible Applications for Implicit Solvent Models

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Computational Science and Its Applications – ICCSA 2005 (ICCSA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3480))

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Abstract

A new approach to identify solvent-exposed atoms in a protein and determine approximate locations of contacted water molecules is presented. The idea of the method is to generate for each atom of the protein molecule a surface grid consisting of twelve uniformly distributed points. These points describe potential locations of water molecules closely packed around an isolated atom. The grid surface coordinates are updated before each energy evaluation step by random rotation of the grid around the atom center. Each grid point is then checked with regard to its accessibility by water and the corresponding hydration status is assigned to it. Thus the information about the hydration degree of each protein atom and the positions of surrounding water molecules becomes available for energy evaluation procedure.

Possible applications of the described method for implicit solvent models accounting for hydrophobic effect, electrical and van der Waals constituents of free energy of solvation, media-dependent electrical permittivity as well as hydrogen bonding with water are outlined.

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Authors and Affiliations

  1. Institute of Mathematics, Technical University of Berlin, Strasse des 17. Juni 136, 10623, Berlin, Germany

    Anna Shumilina

Authors
  1. Anna Shumilina
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Editors and Affiliations

  1. Department of Mathematics and Computer Science, University of Perugia, via Vanvitelli, 1, I-06123, Perugia, Italy

    Osvaldo Gervasi

  2. Department of Computer Science, University of Calgary, 2500 University Drive N.W, T2N 1N4, Calgary, AB, Canada

    Marina L. Gavrilova

  3. William Norris Professor, Head of the Computer Science and Engineering Department, University of Minnesota, USA

    Vipin Kumar

  4. Department of Chemistry, University of Perugia, Via Elce di Sotto, 8, P.O. Box, I-06123, Perugia, Italy

    Antonio Laganà

  5. Institute of High Performance Computing, IHCP, 1 Science Park Road, 01-01 The Capricorn, Singapore Science Park II, 117528, Singapore

    Heow Pueh Lee

  6. School of Computing, Soongsil University, Seoul, Korea

    Youngsong Mun

  7. Clayton School of IT, Monash University, 3800, Clayton, Australia

    David Taniar

  8. OptimaNumerics Ltd, P.O. Box, Belfast, United Kingdom

    Chih Jeng Kenneth Tan

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© 2005 Springer-Verlag Berlin Heidelberg

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Shumilina, A. (2005). A Fast Method for Determination of Solvent-Exposed Atoms and Its Possible Applications for Implicit Solvent Models. In: Gervasi, O., et al. Computational Science and Its Applications – ICCSA 2005. ICCSA 2005. Lecture Notes in Computer Science, vol 3480. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11424758_112

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  • DOI: https://doi.org/10.1007/11424758_112

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25860-5

  • Online ISBN: 978-3-540-32043-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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