ANNOUNCEMENT: MODELLER-3 AVAILABLE (HOMOLOGY PROTEIN MODELING)

Andrej Sali sali
Mon Feb 12 13:41:34 EST 1996


ANNOUNCEMENT:

A NEW VERSION OF MODELLER, A PROGRAM FOR COMPARATIVE PROTEIN STRUCTURE
MODELING, IS RELEASED.

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                                 MODELLER
          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.

** DESCRIPTION:

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.

** DISTRIBUTION:

MODELLER is available free of charge to academic non-profit institutions.

First, please use the anonymous ftp account on guitar.rockefeller.edu
(IP 129.85.13.198) 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.


** CONTENTS:

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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