Software to build 3D structure based on homology?

Andrej Sali sali
Fri Dec 1 17:30:16 EST 1995

                       MODELLER 12, December 31, 1994
                    Copyright(c) 1989-1994 Andrej Sali           
                            All Rights Reserved                  

                           Written by Andrej Sali                
             Birkbeck College, University of London, London, UK  
                 Imperial Cancer Research Fund, London, UK       
                     Harvard University, Cambridge, USA          

Andrej Sali, Box 270, The Rockefeller University, 1230 York Avenue,
New York, NY 10021, USA. Tel: (212) 327 7550. Fax: (212) 327 7540.
E-mail: sali at


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 
(IP or to copy at least 
the following files from the pub/modeller directory to your computer: 
the license form (PostScript file, the encrypted 
distribution file that contains the data files necessary to run MODELLER
(, and an executable for each machine type
and memory size that you need (described in file INSTALLATION).  Next,
print, sign, and mail or fax the license form to Andrej Sali. You will
then receive the encryption key (MODELLER_KEY) with which you will be
able to unpack the encrypted distribution file.  See file INSTALLATION
for installation instructions.

An interface to MODELER is available as part of QUANTA, an interactive
molecular modeling program with many tools for protein modeling and
structural analysis. QUANTA also includes interfaces to CHARMm for
molecular dynamics simulations and X-PLOR for NMR and X-ray structure
determination. QUANTA provides a useful graphical interface to MODELLER 
that facilitates 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 by
QUANTA/MODELLER combination. If you are interested in QUANTA, please
contact Ms. Jo Ellen Collins at Molecular Simulations Inc, 16 New England
Executive Park, Burlington, MA 01803-5297, tel: (617) 229 9800,
fax: (617) 229 9899, email: jcollins at


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; 
modeller12.README  this file;
INSTALLATION       how to install MODELLER;
Install            compilation and installation script relying on Makefile;
tests\             tests and examples;


Andrej Sali
The Rockefeller University, Box 270
1230 York Avenue, New York, NY 10021-6399 
voice (212) 327 7550; fax (212) 327 7540 
e-mail sali at

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