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Journal of Computer-Aided Molecular Design

, Volume 18, Issue 6, pp 401–419 | Cite as

BODIL: a molecular modeling environment for structure-function analysis and drug design

  • Jukka V. Lehtonen
  • Dan-Johan Still
  • Ville-v. Rantanen
  • Jan Ekholm
  • Dag Björklund
  • Zuhair Iftikhar
  • Mikko Huhtala
  • Susanna Repo
  • Antti Jussila
  • Jussi Jaakkola
  • Olli Pentikäinen
  • Tommi Nyrönen
  • Tiina Salminen
  • Mats Gyllenberg
  • Mark S. Johnson
Article

Abstract

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html

density docking molecular visualization sequence comparisons structure comparison structure modeling 

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Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Jukka V. Lehtonen
    • 1
  • Dan-Johan Still
    • 1
  • Ville-v. Rantanen
    • 1
  • Jan Ekholm
    • 1
  • Dag Björklund
    • 1
  • Zuhair Iftikhar
    • 1
  • Mikko Huhtala
    • 1
  • Susanna Repo
    • 1
  • Antti Jussila
    • 2
  • Jussi Jaakkola
    • 2
  • Olli Pentikäinen
    • 1
  • Tommi Nyrönen
    • 3
  • Tiina Salminen
    • 1
  • Mats Gyllenberg
    • 2
    • 4
  • Mark S. Johnson
    • 1
  1. 1.Department of Biochemistry and PharmacyÅbo Akademi UniversityFinland
  2. 2.Department of MathematicsUniversity of TurkuFinland
  3. 3.CSC, the Finnish IT Center for ScienceEspooFinland
  4. 4.Department of Mathematics and Statistics, Rolf Nevanlinna InstituteUniversity of HelsinkiFinland

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