Cavity programs: Difference between revisions

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[[Image:Moleonline-6zgi.png|240px]]

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[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Channels are represented as chains of overlapping spheres, thus radially symmetric. Visualization in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-α trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.

[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Best results are obtained when starting points are specified, which can be obtained from the ''Catalytic Site Atlas'' (CSA). Channels are represented as chains of overlapping spheres, thus radially symmetric. Visualization is in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-α trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.

Results can be downloaded in many formats, including for PyMOL, VMD, and Chimera. When PDB format is downloaded, a channel is represented by atoms of element 'X', group 'TUN', with sequence number = tunnel ID.

Personal experience: When SARS-CoV-2 spike protein [[6zgi]] was submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. This was with the default ''Cavity parameter: probe radius'' of 5 Å. No ''tunnels'' were detected with that parameter set to 1.4 or 2.0 Å.

Cavity programs: Difference between revisions

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@@ Line 88: / Line 88: @@
 [[Image:Moleonline-6zgi.png|240px]]
 </td></tr></table>
-[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Channels are represented as chains of overlapping spheres, thus radially symmetric. Visualization in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-&alpha; trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.
+[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Best results are obtained when starting points are specified, which can be obtained from the ''Catalytic Site Atlas'' (CSA). Channels are represented as chains of overlapping spheres, thus radially symmetric. Visualization is in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-&alpha; trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.
+Results can be downloaded in many formats, including for PyMOL, VMD, and Chimera. When PDB format is downloaded, a channel is represented by atoms of element 'X', group 'TUN', with sequence number = tunnel ID.
 Personal experience: When SARS-CoV-2 spike protein [[6zgi]] was submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. This was with the default ''Cavity parameter: probe radius'' of 5 Å. No ''tunnels'' were detected with that parameter set to 1.4 or 2.0 Å.