Software:MODELLER
| Original author(s) | Andrej Sali |
|---|---|
| Developer(s) | University of California, San Francisco, Accelrys |
| Initial release | 1989 |
| Stable release | 10.3
/ July 13, 2022[1] |
| Operating system | Unix, Linux, macOS, Windows |
| Platform | x86, x86-64 |
| Available in | English |
| Type | homology modeling of proteins |
| License | Proprietary: academic nonprofit freeware, commercial software |
| Website | www |
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer).[2][3] It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed 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 which structure has been solved.
The program also incorporates limited functions for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous proteins and thus difficult to predict by homology modeling.
Modeller was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco.[4] It runs on the operating systems Unix, Linux, macOS, and Windows. It is freeware for academic use. Graphical user interfaces (GUIs) 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. Due to Modeller's popularity, several third party GUIs for MODELLER are available:
- EasyModeller is freeware and is one of the earliest third party GUIs for Modeller.[5] Recent version (EasyModeller 4.0) supports Linux and Windows operating system.
- UCSF Chimera has a simple interface to Modeller.
- PyMod is a free and open-source plugin for PyMOL and has a comprehensive interface for Modeller.[6][7] It supports Linux, Windows and macOS.
- MaxMod is a standalone GUI for MODELLER on Windows.[8]
See also
References
- ↑ "MODELLER News". https://www.salilab.org/modeller/news.html.
- ↑ "Modeller: Generation and Refinement of Homology-Based Protein Structure Models". Macromolecular Crystallography, Part D. Methods in Enzymology. 374. 2003. 461–91. doi:10.1016/S0076-6879(03)74020-8. ISBN 9780121827779.
- ↑ "Comparative protein structure modeling of genes and genomes". Annu Rev Biophys Biomol Struct 29: 291–325. 2000. doi:10.1146/annurev.biophys.29.1.291. PMID 10940251.
- ↑ "Comparative protein modelling by satisfaction of spatial restraints". J. Mol. Biol. 234 (3): 779–815. December 1993. doi:10.1006/jmbi.1993.1626. PMID 8254673.
- ↑ Kuntal, B. K., Aparoy, P., & Reddanna, P. (2010). EasyModeller: A graphical interface to MODELLER. BMC research notes, 3(1), 1.
- ↑ "PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL". Bioinformatics 33 (3): 444–446. 2017. doi:10.1093/bioinformatics/btw638. PMID 28158668.
- ↑ "PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL". BMC Bioinformatics 13 (Suppl 4): S2. 2012. doi:10.1186/1471-2105-13-S4-S2. PMID 22536966.
- ↑ "MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models". Journal of Molecular Modeling 21 (2): 1–10. 2015. doi:10.1007/s00894-014-2563-3. PMID 25636267.
External links
- ModWeb
- EasyModeller - A GUI for Modeller.
- UCSF Chimera interface to Modeller
- PyMod - A PyMOL plugin for Modeller
- MINT - A GUI for Modeller
- MaxMod - A standalone GUI for Modeller on Windows.
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