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MODELLER
PROTEIN MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

Copyright(©) 1989-2006 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

Contact: 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@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) 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, 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@msi.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;

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: ftp://ftp.icgeb.trieste.it/pub/modeller



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