The main purpose of the program FANTOM (Fast Newton-Raphson Torsion Angle Minimizer) is to calculate low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments. The user can run energy minimizations and/or Monte Carlo simulations of an empirical energy function. Protein-solvent interaction is included with a fast routine GETAREA for the calculation of accessible surface areas of individual atoms and their gradients. GETAREA can also be accessed as a stand-alone program. FANTOM is suited for the exploration of low energy conformations of cyclic peptides and of flexible loops in proteins as well. In addition to the above uses, with the newly added program EXDIS, FANTOM is an efficient tool for homology modeling of proteins. Another new feature of this realease is the routine PATHWAY, which allows the user to locate a low-energy path in dihedral angle space between two given conformations of a peptide/protein.


  • How to obtain FANTOM
  • Fantom Manual

    A postscript version of FANTOM manual is included with the distribution. We are in the process of making the entire manual available on line.

  • Title page and Contents
  • Chapter 1: Introduction
  • Chapter 2: Installing the program
  • Chapter 3: Input files
  • Chapter 4: Commands to run FANTOM
  • Chapter 5: Output files
  • Chapter 6: Illustrative examples
  • Chapter 7: Error Messages
  • Chapter 8: References
  • Chapter 9: Index of Commands


    About the authors


    Acknowledgements

    This project is supported by the National Science Foundation (Grants DBI-9632326 and DBI-9714937), the Department of Energy of the United States of America (Grant DE-FG03-96ER62267) and the Sealy and Smith Foundation.


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    Chemistry Software Topic


  • Sealy Center for Structural Biology and Molecular Biophysics
  • Computational Biology Research Group
  • Kizhake Soman's home page
  • Numan Oezguen's home page

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    last updated January 6, 2006