Cavity programs: Difference between revisions
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===I. Cavities=== | ===I. Cavities=== | ||
These programs identify any cavities between atoms of the macromolecule, or pockets beneath a smoothed macromolecular surface, that are larger than the probe diameter. '''No starting position need be specified'''. | These programs identify any cavities between atoms of the macromolecule, or pockets beneath a smoothed macromolecular surface, that are larger than the probe diameter. '''No starting position need be specified'''. | ||
*[[#AVP|AVP]] | |||
*[[#CASTp|CASTp]] | *[[#CASTp|CASTp]] | ||
*[[#Jmol|Jmol]] Cavities as isosurfaces. | *[[#Jmol|Jmol]] Cavities as isosurfaces. | ||
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==AVP== | ==AVP== | ||
[http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program): "Voids are defined as | [http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)]: "Voids are defined as | ||
holes in the protein that are not accessible to solvent, but into | holes in the protein that are not accessible to solvent, but into | ||
which a molecule of a given radius (such as a water) can fit. ... Initially a course grid is used (default 1A), but close to the protein a finer grid (default 0.1A) is | which a molecule of a given radius (such as a water) can fit. ... Initially a course grid is used (default 1A), but close to the protein a finer grid (default 0.1A) is | ||
used and off-grid locations are explored." In addition to locating voids, the program assesses packing quality. | used and off-grid locations are explored." In addition to locating voids, the program assesses packing quality. | ||
(<font color="red">To be continued ...</font>) | |||
==CASTp== | ==CASTp== | ||
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First released December, 2020. | First released December, 2020. | ||
==See Also== | |||
*[[Jmol/Cavities pockets and tunnels]] | |||
*[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]] | |||
*[[Jmol/Depth from surface]] | |||
*[[SARS-CoV-2 spike protein fusion transformation]] which discusses the spike protein cavity used as an example above. | |||
==References== | ==References== | ||
<references /> | <references /> | ||
