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 implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including 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. A graphical interface to MODELLER is commercially available from Accelrys, as part of Discovery Studio Modeling 1.1.

Developers

Ben Webb

Categories

Computational Chemistry

Versions

Citations

Eswar et al. Protein structure modeling with MODELLER. Methods in molecular biology (Clifton, NJ) (2008) vol. 426 pp. 145-59

Eswar et al. Comparative protein structure modeling using MODELLER. Current protocols in protein science / editorial board, John E Coligan [et al] (2007) vol. Chapter 2 pp. Unit 2.9

Technical Notes

No graphical interface. To start the program type 'modeller'. There are some tutorials to get you started available at http://salilab.org/modeller/tutorial/ .

License Type

This software is distributed under an Academic license.

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