分子の三次元構造の類似性:方法とアルゴリズム 3D Molecular Similarity : Method and Algorithms

Access this Article

Search this Article

Author(s)

Abstract

This study presents a method and algorithms for calculation of 3D similarity between pairs of chemical structures represented as 3D molecular graphs. Similarity searching in chemical databases is widely used for virtual screening, lead discovery and optimization, and most recently protein amino-acid sequences studies to discover and determine the functionality of a new isolated protein. This method has obvious advantages over other known methods due to the following: (<I>i</I>) the superposition method does not depend on the preliminary alignments of the chemical structures; (<I>ii</I>) entire conformational space is searched without generation of each conformer; (<I>iii</I>) excellent discrimination between geometrical isomers. Although it is a computationally demanding method, recent implementation of maximum clique algorithm and bound smoothing algorithm made possible the optimization of this method and application to similarity searching in chemical databases of non trivial size.

Journal

  • Journal of Computer Chemistry, Japan

    Journal of Computer Chemistry, Japan 5(1), 39-46, 2006-03-15

    Society of Computer Chemistry, Japan

References:  8

  • <no title>

    CRIPPEN G.

    Distance Geometry and Molecular Conformation, 1988

    Cited by (1)

  • <no title>

    EASTHOPE P.

    Bull. Math. Biol. 51, 173-194, 1989

    Cited by (1)

  • <no title>

    STRANGE P. G.

    Brain biochemistry and brain disorders, 1993

    Cited by (1)

  • <no title>

    WADDINGTON J.

    D1 : D2 Dopamine receptor interactions, 1993

    Cited by (1)

  • <no title>

    FLOYD R.

    Communications of the ACM 7, 345, 1962

    Cited by (1)

  • <no title>

    OSTERGARD R. J.

    Discrete Applied Math. 120, 197-207, 2002

    Cited by (1)

  • <no title>

    RAYMOND J.

    Comput. J. 45, 631-644, 2002

    Cited by (1)

  • <no title>

    RAYMOND J.

    J. Chem. Inf. Comput. Sci. 42, 305-316, 2002

    Cited by (1)

Codes

  • NII Article ID (NAID)
    130000056811
  • NII NACSIS-CAT ID (NCID)
    AA11657986
  • Text Lang
    ENG
  • Article Type
    ART
  • ISSN
    13471767
  • NDL Article ID
    7915368
  • NDL Source Classification
    ZP1(科学技術--化学・化学工業) // ZM13(科学技術--科学技術一般--データ処理・計算機)
  • NDL Call No.
    Z74-C857
  • Data Source
    CJP  NDL  J-STAGE 
Page Top