Cavity programs: Difference between revisions
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*A '''channel''' connects two entrances<ref name="caverweb" />. | *A '''channel''' connects two entrances<ref name="caverweb" />. | ||
*A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" /> | *A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" /> | ||
*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>. | *Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref><ref name="avp">The term ''void'' is used for the program [http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)] from the group of Andrew C. R. Martin at University College, London UK.</ref>. | ||
Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a deep pocket can also be termed a tunnel accessing a functional or catalytic site<ref name="damborsky3" /><ref name="kingsley" />. | Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a deep pocket can also be termed a tunnel accessing a functional or catalytic site<ref name="damborsky3" /><ref name="kingsley" />. | ||
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__NOTOC__ | __NOTOC__ | ||
==Cavities vs. Channels== | ==Cavities vs. Channels== | ||
<table style="background-color:#e0e0e0;" class="wikitable"><tr><td> | |||
The programs listed alphabetically below can be categorized as follows. | The programs listed alphabetically below can be categorized as follows. | ||
===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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===III. Other=== | ===III. Other=== | ||
*[[#MAP_CHANNELS|MAP_CHANNELS]] for solvent channels in crystals of macromolecules. | *[[#MAP_CHANNELS|MAP_CHANNELS]] for solvent channels in crystals of macromolecules. | ||
</td></tr></table> | |||
==AVP== | |||
[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 | |||
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. | |||
(<font color="red">To be continued ...</font>) | |||
==CASTp== | ==CASTp== | ||
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The Jmol Java standalone application is downloadable from [http://jmol.org jmol.org]. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia. | The Jmol Java standalone application is downloadable from [http://jmol.org jmol.org]. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia. | ||
Jmol is updated often, most | Jmol is updated often. In December, 2020, the most recent update was November 19, 2020. | ||
<br clear="both"> | <br clear="both"> | ||
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</td><td> | </td><td> | ||
[[Image:Pacupp-6zgi-fine.png|200px]] | [[Image:Pacupp-6zgi-fine.png|200px]] | ||
</td></tr></table> | |||
<br> | |||
<table align="right" width="440" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td> | |||
[[Image:1vot-pacupp-xfine-inside.png|220px]] | |||
</td><td> | |||
[[Image:1vot-pacupp-xfine-measure.png|220px]] | |||
</td></tr><tr><td> | |||
Inhibitor and 3 water oxygens inside cavity. | |||
</td><td> | |||
Cavity measurements. | |||
</td></tr><tr><td colspan="2"> | |||
Catalytic pocket of acetylcholinesterase [[1vot]] containing the inhibitor huperzine A. Colored by depth from the <font color="red">surface entrance</font>. Cavity detail: extra fine. See [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins|how to obtain these views in PACUPP]]. | |||
</td></tr></table> | </td></tr></table> | ||
[http://molviz.org/pacupp PACUPP]], '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.5 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program. | [http://molviz.org/pacupp PACUPP]], '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.5 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program. | ||
PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a spreadsheet-ready text file. Learning the PACUPP commands is much easier than learning Jmol commands. | PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a '''spreadsheet-ready''' text file. Learning the PACUPP commands is much easier than learning Jmol commands. | ||
PACUPP is a Jmol script. It processes 2/3 of the entries in the [[Protein Data Bank]] in ≤15 sec each. For large models such as ribosomes or proteasomes that may take many minutes, PACUPP offers an unattended batch mode. | PACUPP is a Jmol script. It processes 2/3 of the entries in the [[Protein Data Bank]] in ≤15 sec each. For large models such as ribosomes or proteasomes that may take many minutes, PACUPP offers an unattended batch mode. | ||
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 /> | ||
