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Molecular Engineering

, Volume 5, Issue 1–3, pp 271–300 | Cite as

Practical tools for molecular modeling of complex carbohydrates and their interactions with proteins

  • Serge Pérez
  • Christophe Meyer
  • Anne Imberty
Article

Abstract

Computer modeling has become a valuable component of studies of carbohydrate three-dimensional structures and their relationship to function and properties. In this paper we examine the methods required for conformational modeling of carbohydrates, and we present a series of tools that have been developed to this end. These tools can be integrated into three-dimensional real-time molecular modeling software. A data base of pre-optimized carbohydrate fragments has been established to be used further in the construction of much more complex molecules. In addition we describe some possible uses of a data base of three dimensional structures of the disaccharide fragments present in the glycan moiety ofN-glycoprotein. A molecular mechanical force field appropriate for the conformational analysis of oligosaccharides has been derived by the addition of new parameters to the Tripos force field and is compatible with protein simulations. The new parametrization has been assessed in three stages of increasing complexity: computations of potential energy surfaces, conformational refinement of relevant oligosaccharides, modeling at the atomic level of a protein/carbohydrate complex.

Key words

Carbohydrate lectin modeling interaction force field database 

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Copyright information

© Kluwer Academic Publishers 1995

Authors and Affiliations

  • Serge Pérez
    • 1
  • Christophe Meyer
    • 1
  • Anne Imberty
    • 2
  1. 1.Ingeniérie MoléculaireINRANantes Cédex 03France
  2. 2.Laboratoire de Synthèse Organique-CNRSFaculté des SciencesNantes Cédex 03France

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