Modeller-4, a program for Comparative Protein Structure Modeling

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.

What's new?

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 .cshrcfile). There is no need to resend the licensing agreement.

Availability

MODELLER is available free of charge to academic non-profit institutions. MODELLER is written in Fortran and is meant to run on a UNIX system. 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:

1. the license form (PostScript file academic-license.ps),
2. the distribution file that contains the data files necessary to run MODELLER (modeller4-data.tar.Z),
3. 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 (see below). 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.

Information provided by: Roberto Sánchez

Resources and further information

• The Rockefeller University
  http://www.rockefeller.edu/
• Laboratory of Molecular Biophysics
  http://guitar.rockefeller.edu/
• MODELLER-4 homepage
  http://guitar.rockefeller.edu/modeller/modeller.html
• Download MODELLER-4
  ftp://guitar.rockefeller.edu/pub/modeller/
• Contact information:
  Andrej Sali, Assistant Professor
  The Rockefeller University, Box 270
  1230 York Avenue, New York, NY 10021-6399
  Phone: +1 (212) 327-7550
  Fax: +1 (212) 327-7540

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