Geometric modeling applications in rational drug design: a survey

https://doi.org/10.1016/j.cagd.2006.03.003Get rights and content

Abstract

Computer aided design methods are starting to gain acceptance in the field of life sciences and drug discovery, thus giving rise to a discipline coined Computer Aided Drug Discovery (CADD). This trend is accompanied by a larger interest in 3-dimensional methods. Traditionally for many applications chemical entities such as proteins and molecules have been regarded as either 2D graphs or sequences of letters (proteins and genome). This survey article will give an overview and historical perspective of the state of the art of geometric modeling as it relates to drug discovery.

References (56)

  • G.A. Arteca et al.

    Shape characterization of some molecular model surfaces

    Journal of Computational Chemistry

    (1988)
  • Bajaj C., Lee H.Y., Merkert R. Pascucci V., 1997. Nurbs based b-rep models for macromolecules and their properties. In:...
  • J. Blinn

    A generalization of algebraic surface drawing

    ACM Transactions on Computer Graphics

    (1982)
  • T.L. Blundell et al.

    Knowledge-based prediction of protein structures and the design of novel molecules

    Nature

    (1987)
  • C. Branden et al.

    Introduction to Protein Structure

    (1999)
  • M. Carson

    Wavelets and molecular structure

    Journal of Computer-Aided Molecular Design

    (1996)
  • P.L. Chau et al.

    Molecular recognition: 3d surface structure comparison by gnomonic projection

    Journal of Molecular Graphics

    (1987)
  • H.I. Choi et al.

    The medial axis transform

  • M.L. Connolly

    Solvent-accessible surfaces of proteins and nucleic acids

    Science

    (1983)
  • M.L. Connolly

    Analytical molecular surface calculation

    Journal of Applied Crystallography

    (1983)
  • G.M. Crippen et al.

    Distance Geometry and Molecular Conformation

    (1988)
  • H. Edelsbrunner et al.

    Three-dimensional alpha shapes

    ACM Transactions on Graphics

    (1994)
  • Finkelstein A., Salesin D., 1994. Multiresolution curves. In: ACM Proceedings SIGGRAPH, pp....
  • K.D. Gibson et al.

    Revised algorithm for the build-up procedure for predicting protein conformations by energy minimization

    Journal of Computational Chemistry

    (1987)
  • B. Goldman et al.

    Quadratic shape descriptors. 1. Rapid superposition of dissimilar molecules using geometrically invariant surface descriptors

    Journal of Chemical Information and Computer Sciences

    (2000)
  • D.S. Goodsell et al.

    Automated docking of substrates to proteins by simulated annealing

    Proteins: Structure, Function, and Genetics

    (1990)
  • P. Gund

    Evolution of the pharmacophore concept in pharmaceutical research

  • X. Hao et al.

    Geometry-guided computation of 3d electrostatics for large molecular datasets

    Computer Aided Geometric Design

    (2006)
  • Cited by (0)

    View full text