Lesson plan
MODELLER
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). 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. 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.…
Article summary
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). 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. 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.…
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Discussion questions
- Summarise the article in your own words. Which single claim would you verify first, and why?
- Which claim in this article is most likely to be revised as the sources update? How would you check its current status?
- If two sources disagreed about one of these facts, what would you need in order to trust one over the other?
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