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MOLMOL: a program for display and analysis of macromolecular structures

R Koradi1, M Billeter, K Wüthrich

  • 1Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zurich, Switzerland.

Journal of Molecular Graphics
|February 1, 1996
PubMed
Summary
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MOLMOL is a molecular graphics program designed for analyzing biological macromolecule structures, particularly from nuclear magnetic resonance (NMR) data. It offers advanced visualization and manipulation tools for protein and nucleic acid conformation analysis.

Area of Science:

  • Structural biology
  • Biophysics
  • Computational chemistry

Background:

  • Accurate visualization and analysis of macromolecular structures are crucial for understanding biological function.
  • Nuclear Magnetic Resonance (NMR) spectroscopy provides detailed information on protein and nucleic acid structures in solution.
  • Handling and interpreting the ensemble of conformers from NMR data presents unique challenges.

Purpose of the Study:

  • To introduce MOLMOL, a versatile molecular graphics program tailored for the display, analysis, and manipulation of 3D biological macromolecule structures.
  • To provide specialized tools for processing and visualizing NMR-derived structural ensembles.
  • To enhance the interactive analysis of protein and nucleic acid structures.

Main Methods:

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  • Development of a graphical user interface with menus, dialog boxes, and online help for intuitive operation.
  • Implementation of diverse display options, including conventional and novel schematic representations, with multi-view capabilities.
  • Integration of tools for direct manipulation of covalent structures (atom/bond addition/removal) and 3D structure manipulation (rotations).

    • Main Results:

    • MOLMOL facilitates the display and analysis of typical NMR structural ensembles (20-40 conformers).
    • Includes functions for superimposing conformer sets and calculating root mean square distance (RMSD) values.
    • Provides tools for hydrogen bond identification, NMR constraint violation checking, and listing short interatomic distances.

    Conclusions:

    • MOLMOL is an effective tool for the comprehensive analysis of macromolecular structures, especially those determined by NMR.
    • The program's features aid in the interpretation of structural ensembles and validation of NMR-derived models.
    • MOLMOL enhances the workflow for researchers studying protein and nucleic acid structures.