Cavity programs: Difference between revisions
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==CASTp== | ==CASTp== | ||
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<span style="font-size:120%; font-weight:bold;">CASTp:</span><br>Membrane-proximal cavity in the [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]) shown as a translucent envelope in blue (CASTp default probe radius, 1.4 Å). The membrane-proximal cavity (bottom) is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. | |||
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[[Image:Castp-6zgi.png|200px]] | |||
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[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>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>) | [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>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>) | ||
Displays protein sequences indicating which residues line the displayed cavities. Clicking on a residue centers the 3D view accordingly. | Displays protein sequences indicating which residues line the displayed cavities. Clicking on a residue centers the 3D view accordingly. | ||
Web server visualization is in 3Dmol.js, which seems to offer no user-customizable options beyond rotate and zoom, such as centering or hiding the protein cartoon. | |||
CASTp 3.0 published summer, 2018<ref>PMID: 29860391</ref>. Available as a web server, and a PyMOL plugin. Results can be downloaded for offline viewing with the PyMOL plugin. | CASTp 3.0 published summer, 2018<ref>PMID: 29860391</ref>. Available as a web server, and a PyMOL plugin. Results can be downloaded for offline viewing with the PyMOL plugin. | ||
