Last Modified: Tuesday, 21-Oct-2008 08:53:14 EDT

MODELLER

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.

MODELLER can also perform additional tasks: de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

(Excerpted from the MODELLER home page.)

To use MODELLER in the CSB core, type the following:

setup modeller (or source /srv/local/setup/modeller.set)

mod [scriptname]

or

mod[VERSION] [scriptname] (e.g., mod9v5)

or on Linux, to get more into the underlying Python:

modpy.sh python [scriptname]

The online manual explains what the program can do. There is also a locally-available PDF version.

For a tutorial click here.

Additional information is available at the MODELLER website.

Please Note: In publications of work that made use of MODELLER, please cite the following:

A. Sali and T. L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

Last Modified: Tuesday, 21-Oct-2008 08:53:14 EDT