Cavity programs: Difference between revisions

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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" />.

The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection~~. Programs are listed alphabetically~~.

The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection.

__NOTOC__

==Cavities vs. Channels==

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

===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.

*

==CASTp==

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

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

[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown.

[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown. '''No starting position is required'''. The probe radius (default 1.4 Å) is adjustable.

Displays protein sequences indicating which residues line the displayed cavities. Clicking on a residue centers the 3D view accordingly.

Cavity programs: Difference between revisions

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@@ Line 9: / Line 9: @@
 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" />.
-The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. Programs are listed alphabetically.
+The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection.
 __NOTOC__
+==Cavities vs. Channels==
+The programs listed alphabetically below can be divided into two categories.
+===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.
+*
 ==CASTp==
 <table align="right" width="570" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td>
@@ Line 21: / Line 27: @@
 [[Image:Castp-6zgi.png|200px]]
 </td></tr></table>
-[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown.
+[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown. '''No starting position is required'''. The probe radius (default 1.4 Å) is adjustable.
 Displays protein sequences indicating which residues line the displayed cavities. Clicking on a residue centers the 3D view accordingly.