Roberto Sanchez roberto at GUITAR.ROCKEFELLER.EDU
Sun Feb 25 19:18:23 EST 1996

A mirror site for the distribution of MODELLER (A Protein Structure 
Modeling Program) was established in europe at the International Centre 
for Genetic Engineering and Biotechnology (ICGEB) Trieste, Italy:


The announcement of MODELLER release 3 follows:

                      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 or on the european mirror site at ftp.icgeb.trieste.it
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 as well as analysis of the results produced by MODELLER; 
in particular, the preparation of an alignment and evaluation of the models 
are made much easier. 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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