Roberto Sanchez sancher at rockvax.rockefeller.edu
Mon Jun 16 20:20:21 EST 1997



Please see the README file below for how to get the program.

New features include faster execution, a better manual, more robust
modeling of protein structure. A Linux version is also available.

Current users can use the same keyword as for version 3 (you can find 
it in your .cshrc file). There is no need to resend the licensing 

Best Wishes, Andrej Sali


A review of CASP2 that qualifies MODELLER: R.L. Dunbrack~Jr., D.L. Gerloff, 
M. Bower, X. Chen, O. Lichtarge & F.E. Cohen. Meeting review: the second 
meeting on the critical assessment of techniques for protein structure 
prediction (CASP2), Asilomar California, December 13-16, 1996. Folding & 
Design 2, R27-R42, 1997.


                      MODELLER 4, June 15, 1997
                    Copyright(c) 1989-1997 Andrej Sali           
                            All Rights Reserved                  

        Written by Andrej Sali, Roberto Sanchez, and Azat Badretdinov
                   Rockefeller University, New York, USA
                     Harvard University, Cambridge, USA
                 Imperial Cancer Research Fund, London, UK       
             Birkbeck College, University of London, London, UK  

Andrej Sali, The Rockefeller University, 1230 York Avenue, New York,
NY 10021, USA. Tel: +1-212-327-7550. Fax: +1-212-327-7540 (or 7974).
E-mail: sali at rockvax.rockefeller.edu. URL: http://guitar.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 150-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 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 (modeller4-data.tar.Z), and an executable 
for each machine type that you want to use (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_MODELLER4 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, InsightII,
and WEBLab, interactive molecular modeling programs with many tools for protein 
modeling and structural analysis. QUANTA, InsightII, and WEBLab 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 
these programs, please contact Ms. Brenda Pfeiffer, Molecular Simulations Inc.,
9685 Scranton Road, San Diego, CA  92121-3752, tel: +1-619-546-5319,
fax: +1-619-458-0136, email: blp at msi.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; 
modeller4.README   this file;
INSTALLATION       how to install MODELLER;
Install            compilation and installation script relying on Makefile;
examples\          examples;


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