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.
Sealy Center for Structural
Biology and Molecular Biophysics
Computational Biology Research Group
Kizhake Soman's home page
Numan Oezguen's home page
Site created by Robert Fraczkiewicz; maintained by Surendra Negi
last updated January 6, 2006
