MODELLER

MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures (rarer).[1][2] 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 a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino 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 the University of California, San Francisco.[3] Although it is freely available for academic use, graphical user interfaces and commercial versions are distributed by Accelrys. The ModWeb comparative protein structure modeling webserver is based on MODELLER and other tools for automatic protein structure modeling, with an option to deposit the resulting models into ModBase. A freely available GUI to MODELLER called EasyModeller is developed by Kuntal Kumar Bhusan at University Of Hyderabad,India. A new version of EasyModeller (EasyModeller 4.0) has been recently released and available for free download for Linux and Windows OS. There is also a simple interface to MODELLER in the program UCSF Chimera.

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References

  1. ↑ Fiser A, Sali A (2003). "Modeller: generation and refinement of homology-based protein structure models". Meth. Enzymol. 374: 461–91. doi:10.1016/S0076-6879(03)74020-8. PMID 14696385.
  2. ↑ Martí-Renom MA, Stuart AC, 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. doi:10.1146/annurev.biophys.29.1.291. PMID 10940251.
  3. ↑ Sali A, Blundell TL (December 1993). "Comparative protein modelling by satisfaction of spatial restraints". J. Mol. Biol. 234 (3): 779–815. doi:10.1006/jmbi.1993.1626. PMID 8254673.