Structure superposition tools: Difference between revisions
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===Example for Rigid Alignment=== | ===Example for Rigid Alignment=== | ||
[[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin found in [[1tub]] chain A, length 440. However, the sequence similarity is very low. | [[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin found in [[1tub]] chain A, length 440. However, the sequence similarity is very low. | ||
====CE==== | ====CE example==== | ||
*3.2 Å RMSD for 305 residues. The structural alignment has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less. | *3.2 Å RMSD for 305 residues. The structural alignment has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less. | ||
*Z-score: 6.5. | *Z-score: 6.5. | ||
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*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software (see above). | *Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software (see above). | ||
====Dali==== | ====Dali example==== | ||
*3.2 Å RMSD RIGID alignment included 299 residues. | *3.2 Å RMSD RIGID alignment included 299 residues. | ||
*Z-score: 25.5. | *Z-score: 25.5. | ||
*The structure-based sequence alignment has many gaps. | *The structure-based sequence alignment has many gaps. | ||
====FATCAT==== | ====FATCAT example==== | ||
*3.02 Å RMSD RIGID alignment includes 298 residues. | *3.02 Å RMSD RIGID alignment includes 298 residues. | ||
*P value: 5 x 10<sup>-8</sup> (used instead of z-score to take twists into account). | *P value: 5 x 10<sup>-8</sup> (used instead of z-score to take twists into account). | ||
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*The structure-based sequence alignment has many gaps, looking similar to that generated by CE. | *The structure-based sequence alignment has many gaps, looking similar to that generated by CE. | ||
====MAMMOTH==== | ====MAMMOTH example==== | ||
*4.0 Å (?) with 298 aligned residues (?) (Labeling in results is unclear.) | *4.0 Å (?) with 298 aligned residues (?) (Labeling in results is unclear.) | ||
*Structure-based sequence alignment is displayed. | *Structure-based sequence alignment is displayed. | ||
====TM-Align==== | |||
====TM-Align example==== | |||
*3.42 Å for 312 aligned residues. | *3.42 Å for 312 aligned residues. | ||
*Structure-based sequence alignment is displayed. | *Structure-based sequence alignment is displayed. | ||
====TopMatch==== | |||
====TopMatch example==== | |||
*Error # 1063, no explanation. No structures displayed in Jmol. | *Error # 1063, no explanation. No structures displayed in Jmol. | ||
*3.1 Å RMSD. Alignment includes 251 residues. Sequence identity in the aligned regions is 12%. | *3.1 Å RMSD. Alignment includes 251 residues. Sequence identity in the aligned regions is 12%. | ||
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*Tried the example requiring flexibility (above) as a second case. A 40 residue subdomain was aligned with RMSD 1.8 Å, and the alignment was displayed in Jmol with no error. | *Tried the example requiring flexibility (above) as a second case. A 40 residue subdomain was aligned with RMSD 1.8 Å, and the alignment was displayed in Jmol with no error. | ||
====VAST==== | ====VAST example==== | ||
* 4.0 Å RMSD for 299 aligned residues. | * 4.0 Å RMSD for 299 aligned residues. | ||
* Expectation value: 10<sup>-16</sup>. | * Expectation value: 10<sup>-16</sup>. | ||
