- MODELLER
MODELLER is a
computer program used in producing homology models ofprotein tertiary structure s as well asquaternary structure s (rarer). It implements a technique inspired by nuclear magnetic resonance known as "satisfaction of spatial restraints", by which a set of geometrical criteria are used to create aprobability density function for the location of eachatom in the protein. The method relies on an inputsequence alignment between the targetamino acid sequence to be modeled and a template protein whose structure has been solved.The program also incorporates limited functionality for
ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous proteins and therefore difficult to predict by homology modeling.MODELLER was originally written and is currently maintained by
Andrej Sali at theUniversity of California, San Francisco . Although it is freely available for academic use,graphical user interface s and commercial versions are distributed byAccelrys .External links
* [http://salilab.org/modeller/ MODELLER]
References
* Sali A, Blundell TL. (1993). Comparative protein modelling by satisfaction of spatial restraints. "J. Mol. Biol." 234, 779-815.
* Marti-Renom MA, Stuart A, Fiser A, Sánchez R, Melo F, Sali A. (2000). Comparative protein structure modeling of genes and genomes. "Annu. Rev. Biophys. Biomol. Struct." 29, 291-325.
* Fiser A, Sali A. (2003) Modeller: generation and refinement of homology-based protein structure models. "Methods Enzymol." 374:461-91
Wikimedia Foundation. 2010.