“MODELLER”的意思、由来-开放百科全书

Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer).^[1]^[2] 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.^[3] 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:

See also

External links

References

1. ^{{Cite book |vauthors=Fiser A, Sali A |title=Modeller: generation and refinement of homology-based protein structure models |journal=Meth. Enzymol. |volume=374 |issue= |pages=461–91 |year=2003 |pmid=14696385 |doi=10.1016/S0076-6879(03)74020-8 |url=|series=Methods in Enzymology |isbn=9780121827779 }}
2. ^{{cite journal |vauthors=Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A |title=Comparative protein structure modeling of genes and genomes |journal=Annu Rev Biophys Biomol Struct |volume=29 |issue= |pages=291–325 |year=2000 |pmid=10940251 |doi=10.1146/annurev.biophys.29.1.291 |url=}}
3. ^{{cite journal |vauthors=Sali A, Blundell TL |title=Comparative protein modelling by satisfaction of spatial restraints |journal=J. Mol. Biol. |volume=234 |issue=3 |pages=779–815 |date=December 1993 |pmid=8254673 |doi=10.1006/jmbi.1993.1626 |url=}}
4. ^Kuntal, B. K., Aparoy, P., & Reddanna, P. (2010). EasyModeller: A graphical interface to MODELLER. BMC research notes, 3(1), 1.
5. ^{{cite journal| pmid=28158668 | doi=10.1093/bioinformatics/btw638 | volume=33 | issue=3 | title=PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL | year=2017 | journal=Bioinformatics | pages=444–446 | vauthors=Janson G, Zhang C, Prado MG, Paiardini A}}
6. ^{{cite journal| pmid=22536966 | doi=10.1186/1471-2105-13-S4-S2 | volume=13 Suppl 4 | title=PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL | pmc=3303726 | year=2012 | journal=BMC Bioinformatics | page=S2 | vauthors=Bramucci E, Paiardini A, Bossa F, Pascarella S}}
7. ^{{cite journal | vauthors = Parida BK, Panda PK, Misra N, Mishra BK | year = 2015 | title = MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models | journal = Journal of Molecular Modeling | volume = 21 | issue = 2| pages = 1–10 | doi=10.1007/s00894-014-2563-3| pmid = 25636267 }}