Cavity programs: Difference between revisions

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*A '''channel''' connects two entrances<ref name="caverweb" />.

*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" />.

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__NOTOC__

==Cavities vs. Channels==

The programs listed alphabetically below can be ~~divided into two categories~~.

The programs listed alphabetically below can be categorized as follows.

===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~~. Identification is objective~~. '''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]]

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

*[[#PACUPP|PACUPP]] Cavities filled with pseudoatoms.

===II. Channels/Tunnels===

These programs '''require that one or more starting locations be specified'''. Thus, they may not identify cavities unrelated to the specified starting point(s). They look for channels/tunnels connecting a starting point with the surface, or with a specified end point.

*[[#CAVER|CAVER]] Personal note: unable to run program in macOS or Windows 10.

*[[#CAVER|CAVER]] ''Personal note: unable to run program in macOS or Windows 10 (December, 2020).''

*[[#CAVER Web|CAVER Web]] ''Appeared to be '''out of order''' in December, 2020.''

*[[#ChExVis|ChExVis]] Limited to channels with 2 entrances.

*[[#MolAxis|MolAxis]] ''Server appeared to be '''out of order''' in December, 2020.''

*[[#MOLEonline|MOLEonline]]

===III. Other===

*[[#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==

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[[Image:Jmol-cavities-6zgi-1.4-10.png|200px]]

</td></tr></table>

[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands.

[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands. Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.2 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. '''Pockets''' are depicted with open mouths (illustrated here: pink, orange, yellow, blue); '''Interior Cavities''' (buried cavities; voids) are depicted as closed isosurfaces (illustrated here: green).

Jmol has an extensive command language that provides great flexibility in visualizing cavities. However, displaying more than one isosurface fragment at a time, and coloring the fragments differently (as in the left snapshot) is cumbersome.

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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.

Jmol is updated often, most ~~recently~~ November 19, 2020.

Jmol is updated often. In December, 2020, the most recent update was November 19, 2020.

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[[Image:Pacupp-6zgi-fine.png|200px]]

</td></tr></table>

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" />). 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.

<br>

[[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>

[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.

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==

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@@ Line 5: / Line 5: @@
 *A '''channel''' connects two entrances<ref name="caverweb" />.
 *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" />.
@@ Line 12: / Line 12: @@
 __NOTOC__
 ==Cavities vs. Channels==
-The programs listed alphabetically below can be divided into two categories.
+<table style="background-color:#e0e0e0;" class="wikitable"><tr><td>
+The programs listed alphabetically below can be categorized as follows.
 ===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. Identification is objective. '''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]]
+*[[#Jmol|Jmol]] Cavities as isosurfaces.
+*[[#PACUPP|PACUPP]] Cavities filled with pseudoatoms.
 ===II. Channels/Tunnels===
 These programs '''require that one or more starting locations be specified'''. Thus, they may not identify cavities unrelated to the specified starting point(s). They look for channels/tunnels connecting a starting point with the surface, or with a specified end point.
-*[[#CAVER|CAVER]] Personal note: unable to run program in macOS or Windows 10.
+*[[#CAVER|CAVER]] ''Personal note: unable to run program in macOS or Windows 10 (December, 2020).''
+*[[#CAVER Web|CAVER Web]] ''Appeared to be '''out of order''' in December, 2020.''
+*[[#ChExVis|ChExVis]] Limited to channels with 2 entrances.
+*[[#MolAxis|MolAxis]] ''Server appeared to be '''out of order''' in December, 2020.''
+*[[#MOLEonline|MOLEonline]]
+===III. Other===
+*[[#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==
@@ Line 76: / Line 96: @@
 [[Image:Jmol-cavities-6zgi-1.4-10.png|200px]]
 </td></tr></table>
-[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands.
+[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands. Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.2 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. '''Pockets''' are depicted with open mouths (illustrated here: pink, orange, yellow, blue); '''Interior Cavities''' (buried cavities; voids) are depicted as closed isosurfaces (illustrated here: green).
 Jmol has an extensive command language that provides great flexibility in visualizing cavities. However, displaying more than one isosurface fragment at a time, and coloring the fragments differently (as in the left snapshot) is cumbersome.
@@ Line 82: / Line 102: @@
 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 recently November 19, 2020.
+Jmol is updated often. In December, 2020, the most recent update was November 19, 2020.
 <br clear="both">
@@ Line 115: / Line 135: @@
 [[Image:Pacupp-6zgi-fine.png|200px]]
 </td></tr></table>
-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" />). 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.
+<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>
+[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 &le;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.
+==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 />