Cavity programs - Revision history

Eric Martz: /* See Also */

2021-01-28T01:42:19Z

Eric Martz: /* References */

2021-01-28T00:38:30Z

References

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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]]

	==References==		==References==
	<references />		<references />

Eric Martz: /* I. Cavities */

2020-12-19T21:28:03Z

I. Cavities

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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\|AVP]]
	*[[#CASTp\|CASTp]]		*[[#CASTp\|CASTp]]
	*[[#Jmol\|Jmol]] Cavities as isosurfaces.		*[[#Jmol\|Jmol]] Cavities as isosurfaces.

Eric Martz: /* I. Cavities */

2020-12-19T21:27:45Z

I. Cavities

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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]]
	*[[#CASTp\|CASTp]]		*[[#CASTp\|CASTp]]
	*[[#Jmol\|Jmol]] Cavities as isosurfaces.		*[[#Jmol\|Jmol]] Cavities as isosurfaces.

Eric Martz: /* AVP */

2020-12-19T21:23:05Z

AVP

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	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==

Eric Martz: /* AVP */

2020-12-19T21:22:16Z

AVP

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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

Eric Martz: /* CASTp */

2020-12-19T20:39:31Z

CASTp

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	*[[#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>		</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.

	==CASTp==		==CASTp==

Eric Martz at 20:31, 19 December 2020

2020-12-19T20:31:37Z

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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" />.

Eric Martz: /* PACUPP */

2020-12-19T17:32:36Z

PACUPP

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	</td></tr></table>		</td></tr></table>
	<br>		<br>
	<table align="right" width="~~400~~" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td>		<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\|~~200px~~]]		[[Image:1vot-pacupp-xfine-inside.png\|220px]]
	</td><td>		</td><td>
	[[Image:1vot-pacupp-xfine-measure.png\|~~200px~~]]		[[Image:1vot-pacupp-xfine-measure.png\|220px]]
	</td></tr><tr><td>		</td></tr><tr><td>
	Inhibitor and 3 water oxygens inside cavity.		Inhibitor and 3 water oxygens inside cavity.

Eric Martz: /* PACUPP */

2020-12-19T17:28:48Z

PACUPP

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	Cavity measurements.		Cavity measurements.
	</td></tr><tr><td colspan="2">		</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>. See [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins\|how to obtain these views in PACUPP]].		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.

← Older revision		Revision as of 01:42, 28 January 2021
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	*[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]		*[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]
	*[[Jmol/Depth from surface]]		*[[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 />