# MODELLER

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Modeller Original author Andrej Sali Developers University of California, San Francisco, Accelrys Release 1989; 37 years ago (1989) Stable release 10.3 / July 13, 2022; 3 years ago (2022-07-13)[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.salilab.org/modeller/

**Modeller**, often stylized as **MODELLER**, is a [computer program](/source/Computer_program) used for [homology modeling](/source/Homology_modeling) to produce models of [protein](/source/Protein) [tertiary structures](/source/Tertiary_structure) and [quaternary structures](/source/Quaternary_structure) (rarer).[2][3] It implements a method inspired by [nuclear magnetic resonance spectroscopy of proteins](/source/Nuclear_magnetic_resonance_spectroscopy_of_proteins) (protein NMR), termed *[satisfaction of spatial restraints](/source/Homology_modeling#Satisfaction_of_spatial_restraints)*, by which a set of geometrical criteria are used to create a [probability density function](/source/Probability_density_function) for the location of each [atom](/source/Atom) in the protein. The method relies on an input [sequence alignment](/source/Sequence_alignment) between the target [amino acid](/source/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](/source/Ab_initio_structure_prediction) of [loop](/source/Loop_(biochemistry)) regions of proteins, which are often highly variable even among [homologous](/source/Homology_(biology)) proteins and thus difficult to predict by homology modeling.

Modeller was originally written and is currently maintained by [Andrej Sali](/source/Andrej_Sali) at the [University of California, San Francisco](/source/University_of_California%2C_San_Francisco).[4] It runs on the operating systems [Unix](/source/Unix), [Linux](/source/Linux), [macOS](/source/MacOS), and [Windows](/source/Microsoft_Windows). It is [freeware](/source/Freeware) for academic use. [Graphical user interfaces](/source/Graphical_user_interface) (GUIs) and [commercial](/source/Commercial_software) versions are distributed by [Accelrys](/source/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](/source/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](/source/Linux) and [Windows](/source/Microsoft_Windows) operating system.

- [UCSF Chimera](/source/UCSF_Chimera) has a simple interface to Modeller.

- PyMod is a [free and open-source](/source/Free_software) plugin for [PyMOL](/source/PyMOL) and has a comprehensive interface for Modeller.[6][7] It supports [Linux](/source/Linux), [Windows](/source/Microsoft_Windows) and [macOS](/source/MacOS).

- MaxMod is a standalone GUI for MODELLER on [Windows](/source/Microsoft_Windows).[8]

## See also

- [List of protein structure prediction software](/source/List_of_protein_structure_prediction_software)

## References

1. **[^](#cite_ref-1)** ["MODELLER News"](https://www.salilab.org/modeller/news.html). *salilab.org*. Retrieved 2022-11-02.

1. **[^](#cite_ref-pmid14696385_2-0)** Fiser A, Sali A (2003). "Modeller: Generation and Refinement of Homology-Based Protein Structure Models". *Macromolecular Crystallography, Part D*. Methods in Enzymology. Vol. 374. pp. 461–91. [doi](/source/Doi_(identifier)):[10.1016/S0076-6879(03)74020-8](https://doi.org/10.1016%2FS0076-6879%2803%2974020-8). [ISBN](/source/ISBN_(identifier)) [9780121827779](https://en.wikipedia.org/wiki/Special:BookSources/9780121827779). [PMID](/source/PMID_(identifier)) [14696385](https://pubmed.ncbi.nlm.nih.gov/14696385).

1. **[^](#cite_ref-pmid10940251_3-0)** 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](/source/Doi_(identifier)):[10.1146/annurev.biophys.29.1.291](https://doi.org/10.1146%2Fannurev.biophys.29.1.291). [PMID](/source/PMID_(identifier)) [10940251](https://pubmed.ncbi.nlm.nih.gov/10940251).

1. **[^](#cite_ref-pmid8254673_4-0)** Sali A, Blundell TL (December 1993). "Comparative protein modelling by satisfaction of spatial restraints". *J. Mol. Biol*. **234** (3): 779–815. [doi](/source/Doi_(identifier)):[10.1006/jmbi.1993.1626](https://doi.org/10.1006%2Fjmbi.1993.1626). [PMID](/source/PMID_(identifier)) [8254673](https://pubmed.ncbi.nlm.nih.gov/8254673).

1. **[^](#cite_ref-5)** [Kuntal, B. K., Aparoy, P., & Reddanna, P. (2010). EasyModeller: A graphical interface to MODELLER. BMC research notes, 3(1), 1.](http://www.biomedcentral.com/1756-0500/3/226)

1. **[^](#cite_ref-6)** Janson G, Zhang C, Prado MG, Paiardini A (2017). ["PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL"](https://doi.org/10.1093%2Fbioinformatics%2Fbtw638). *Bioinformatics*. **33** (3): 444–446. [doi](/source/Doi_(identifier)):[10.1093/bioinformatics/btw638](https://doi.org/10.1093%2Fbioinformatics%2Fbtw638). [PMID](/source/PMID_(identifier)) [28158668](https://pubmed.ncbi.nlm.nih.gov/28158668).

1. **[^](#cite_ref-7)** Bramucci E, Paiardini A, Bossa F, Pascarella S (2012). ["PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303726). *BMC Bioinformatics*. **13** (Suppl 4): S2. [doi](/source/Doi_(identifier)):[10.1186/1471-2105-13-S4-S2](https://doi.org/10.1186%2F1471-2105-13-S4-S2). [PMC](/source/PMC_(identifier)) [3303726](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303726). [PMID](/source/PMID_(identifier)) [22536966](https://pubmed.ncbi.nlm.nih.gov/22536966).

1. **[^](#cite_ref-8)** Parida BK, Panda PK, Misra N, Mishra BK (2015). "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. [doi](/source/Doi_(identifier)):[10.1007/s00894-014-2563-3](https://doi.org/10.1007%2Fs00894-014-2563-3). [PMID](/source/PMID_(identifier)) [25636267](https://pubmed.ncbi.nlm.nih.gov/25636267). [S2CID](/source/S2CID_(identifier)) [30626573](https://api.semanticscholar.org/CorpusID:30626573).

## External links

- [Official website](https://salilab.org/modeller)

- [ModWeb](https://salilab.org/modweb/)

- [EasyModeller](http://modellergui.blogspot.com/) - A GUI for Modeller.

- [UCSF Chimera interface to Modeller](http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/modeller.html)

- [PyMod](http://schubert.bio.uniroma1.it/pymod/index.html) - A PyMOL plugin for Modeller

- [MINT](http://www.bioinf.org.uk/software/mint/index.html) - A GUI for Modeller

- [MaxMod](http://www.immt.res.in/maxmod/) - A standalone GUI for Modeller on Windows.

v t e Computational chemistry software Cheminformatics Open source Bioclipse Blue Obelisk Chemistry Development Kit ECCE JOELib OELib Open Babel RDKit Proprietary AlvaDesc Canvas Chemicalize Discovery Studio OEChem TK Chemical kinetics Open source APBS Cantera KPP Proprietary Autochem Chemical WorkBench CHEMKIN COSILAB DelPhi Khimera Molecular modelling, visualization List of molecular graphics systems Open source Ascalaph Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol Proprietary Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow EzMol Gaussian Maestro MarvinSketch MarvinView MODELLER Molecular Operating Environment SAMSON Spartan UCSF Chimera VIDA VMD Molecular docking List of protein-ligand docking software Open source AutoDock AutoDock Vina FlexAID rDock Proprietary Glide LeDock Molecular Operating Environment OEDocking Molecular dynamics Open source CP2K GROMACS LAMMPS OpenMM PLUMED Proprietary Abalone AMBER CHARMM CPMD Desmond GROMOS NAMD Quantum chemistry List of quantum chemistry and solid-state physics software Open source ABINIT ACES (CFOUR) AIMAll BigDFT COLUMBUS CONQUEST CP2K Dalton DIRAC DP code FLEUR FreeON MADNESS MOPAC MPQC NWChem Octopus ORCA (academic) OpenMolcas PARSEC PSI PyQuante PySCF Quantum ESPRESSO (PWscf) RMG SIESTA VB2000 YAMBO code Proprietary ADF AMPAC DMol3 CADPAC CASINO CASTEP CPMD CRUNCH CRYSTAL FHI-aims Firefly GAMESS (UK) GAMESS (US) Gaussian Jaguar MOLCAS MOLPRO ONETEP OpenAtom ORCA (industrial) PLATO PQS Q-Chem Quantemol Scigress Spartan TeraChem TURBOMOLE VASP WIEN2k XMVB Skeletal structure drawing Open source JChemPaint Molsketch XDrawChem Proprietary ACD/ChemSketch BIOVIA Draw ChemDoodle ChemDraw ChemWindow JME Molecule Editor MarvinSketch PICTO Others Aqion EXC code GenX GSim Mercury CrystalExplorer ICM (ICM-Browser) Materials Studio Molden OpenChrom SASHIMI

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Adapted from the Wikipedia article [MODELLER](https://en.wikipedia.org/wiki/MODELLER) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/MODELLER?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.