Cavity programs: Difference between revisions
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==PACUPP== | ==PACUPP== | ||
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<span style="font-size:120%; font-weight:bold;">PACUPP:</span><br>Membrane-proximal cavity in the [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]) rendered as pseudoatoms. This cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. | <span style="font-size:120%; font-weight:bold;">PACUPP:</span><br>Membrane-proximal cavity in the [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]) rendered as pseudoatoms. This cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. | ||
*Left: cavity definition = coarse (pseudoatom radius 2.5 Å). | *Left: cavity definition = coarse (pseudoatom radius 2.5 Å). | ||
*Right: cavity definition = fine (pseudoatom radius 1.5 Å), colored by depth from the surface. | *Right: cavity definition = fine (pseudoatom radius 1.5 Å), colored by depth from the surface. | ||
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[[Image:Pacupp-6zgi-coarse.png]] | [[Image:Pacupp-6zgi-coarse.png]] [[Image:Pacupp-6zgi-fine.png|200px]] | ||
</td></tr></table> | </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"). 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, '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"). 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. | ||
