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- Jmol/Cavities pockets and tunnels (22,245 bytes)
2: ... An alternative method for finding and displaying cavities is [[PACUPP]]. Several other methods are summariz...
7: ==How To Show Cavities In Proteopedia==
8: ...o consider an alternative method which represents cavities with pseudoatoms, [[PACUPP]].
11: ...l uses two "rolling" spherical probes to identify cavities.
12: *The smaller ''cavity probe'' detects the cavities. Its default radius is 1.2 Å. For comparison, th... - Image:1IH5 cavities xfine small 2 5 20 24.pdb (83 bytes)
- User:Eric Martz/Cavities tests (2,280 bytes)
10: ...ace "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl";
12: <text>Load isosurface cavities</text>
15: ...mages/6/67/6zgi-cavities.jvxl -- see [[Image:6zgi-cavities.jvxl]])
21: ...oad "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
26: ...iki/index.php/Image:6zgi-cavities.pngj Image:6zgi-cavities.png]) - Image:7pmx-without-381-579 cavities xfine small 2 5 20 24.pdb (0 bytes)
- Image:7pmy-without-403-606 cavities xfine small 2 5 20 24.pdb (0 bytes)
- Image:2j1n cavities fine small 3 5 20 24.pdb (133 bytes)
2: ...orin structure 2j1n with pseudo-atoms filling the cavities, generated by PACUPP. - Image:Cavities and leucine plug abcg2.png (0 bytes)
- Image:2j1n cavities vfine small 2.4 5 20 24.pdb (0 bytes)
- Image:6zgi-cavities.jvxl (0 bytes)
- Image:6zgi-cavities.pngj (0 bytes)
- PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins (8,080 bytes)
2: ...ith pseudoatoms. PACUPP provides tools to isolate cavities of interest and display their contents, their lin...
13: ...ve 2-4 pseudoatoms each. By default, PACUPP hides cavities with <5 pseudoatoms.</ref>. All but one of these ...
17: ...e when the <scene name='86/869942/Pacupp_depth/1'>cavities are colored by PACUPP's "depth" color scheme</sce...
23: ...ings" off of clusters of pseudoatoms representing cavities. These methods are demonstrated in the YouTube vi...
29: ...ws menu also offers a view suitable for measuring cavities. <scene name='86/869942/Dimensions/1'>Here are tw... - Image:Jmol-cavities-6zgi.png (0 bytes)
- Image:Jmol-cavities-6zgi-2.5-10.png (0 bytes)
- Image:Jmol-cavities-6zgi-1.4-10.png (0 bytes)
Page text matches
- 1rrl (4,805 bytes)
24: ...ciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing eve... - 1rrh (4,819 bytes)
24: ...ciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing eve... - 2j21 (9,742 bytes)
26: ...water-accessible crevices or hydrophobic internal cavities with no other structural changes but with a large... - 2j20 (9,816 bytes)
26: ...water-accessible crevices or hydrophobic internal cavities with no other structural changes but with a large... - 1gwg (4,412 bytes)
24: ... surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automati... - 1gwa (4,173 bytes)
24: ... surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automati... - 1gw9 (4,281 bytes)
24: ... surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automati... - 1gwd (4,203 bytes)
22: ... surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automati... - 1aeq (5,642 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aed (5,651 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aes (3,996 bytes)
24: ...ow small molecule penetration into buried protein cavities. - 1aej (5,637 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aek (5,621 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aeo (5,656 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aev (6,008 bytes)
24: ...e specific binding behavior of artificial protein cavities can be harnessed and redirected toward the oxidat... - 1aee (5,619 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aet (4,017 bytes)
24: ...ow small molecule penetration into buried protein cavities. - 1aeb (5,643 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz... - 1aeu (3,986 bytes)
24: ...ow small molecule penetration into buried protein cavities. - 1aeg (5,635 bytes)
24: ...rystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, th...
26: Artificial protein cavities as specific ligand-binding templates: characteriz...
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