ANNOUNCEMENT: MODELLER-3 AVAILABLE (HOMOLOGY PROTEIN MODELING)
Mon Feb 12 13:41:34 EST 1996
A NEW VERSION OF MODELLER, A PROGRAM FOR COMPARATIVE PROTEIN STRUCTURE
MODELING, IS RELEASED.
PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
MODELLER 3, December 31, 1995
Copyright(c) 1989-1995 Andrej Sali
All Rights Reserved
Written by Andrej Sali
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Andrej Sali, Box 270, The Rockefeller University, 1230 York Avenue,
New York, NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540.
E-mail: sali at rockvax.rockefeller.edu.
MODELLER is most frequently used for homology or comparative modeling
of protein three-dimensional structure: the user provides an alignment
of a sequence to be modeled with known related structures and MODELLER
will automatically calculate a full-atom model. More generally, MODELLER
models protein 3D structure by satisfaction of spatial restraints
(A. Sali & T.L. Blundell. J.Mol.Biol. 234, 779-815, 1993). In principle,
the restraints can be derived from a number of different sources. These
include homologous structures (comparative modeling), NMR experiments
(NMR refinement), rules of secondary structure packing (combinatorial
modeling), cross-linking experiments, fluorescence spectroscopy, image
reconstruction in electron microscopy, site-directed mutagenesis,
intuition, residue-residue and atom-atom potentials of mean force, etc.
The output of MODELLER is a 3D structure of a protein that satisfies
these restraints as well as possible. The optimization is carried out
by the variable target function procedure employing methods of conjugate
gradients and molecular dynamics with simulated annealing. MODELLER
can also do several other tasks, including multiple comparison of protein
sequences and/or structures, clustering, and searching of sequence
databases. The program is described in a 120-page manual. MODELLER is
written in Fortran and is meant to run on a UNIX system.
MODELLER is available free of charge to academic non-profit institutions.
First, please use the anonymous ftp account on guitar.rockefeller.edu
(IP 188.8.131.52) to copy at least the following files from the
pub/modeller directory to your computer: the license form (PostScript
file academic-license.ps), the distribution file that contains the data
files necessary to run MODELLER (modeller3-data.tar.Z), and an executable
for each machine type that you need (described in file INSTALLATION).
Next, please sign and mail (or fax) the license form to Andrej Sali. You
will then receive the key (MODELLER_KEY) that has to be assigned to the
environment variable KEY_MODELLER3 in your login script (.cshrc). See file
INSTALLATION for installation instructions.
There is also a MODELLER home page on World Wide Web at URL
http://guitar.rockefeller.edu that can be used to ftp the program and
view the manual.
A graphical interface to MODELLER is available as part of QUANTA and INSIGHT,
interactive molecular modeling programs with many tools for protein modeling
and structural analysis. QUANTA and INSIGHT facilitate preparation of input
files for MODELLER (eg, alignment file) as well as an analysis of results
(eg, an evaluation of the models). If you are interested in QUANTA or INSIGHT,
please contact Ms. Brenda Pfeiffer, BIOSYM / Molecular Simulations Inc.,
9685 Scranton Road, San Diego, CA 92121-3752, tel: +1-619-546-5319,
fax: +1-619-458-0136, email: blp at biosym.com.
src\ sources or executables for MODELLER;
modlib\ libraries and data files for the programs;
scripts\ script files used to compile and use MODELLER;
doc\ MODELLER documentation;
Makefile Makefile for compiling/installing MODELLER modules;
modeller3.README this file;
INSTALLATION how to install MODELLER;
Install compilation and installation script relying on Makefile;
tests\ tests and examples;
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