Structure superposition tools: Difference between revisions
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<tr><td>Topmatch</td><td>416</td><td>1.68 | <tr><td>Topmatch</td><td>416</td><td>1.68 | ||
</td></tr></table> | </td></tr></table> | ||
[[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin<ref>PMID: 9628483</ref><ref>PMID: 20459678</ref> found in [[1tub]] chain A, length 440. However, the sequence identity is low. 92/372 residues can be aligned with 19% identity (2 gaps), and another 14 residue stretch with 42% identity (no gaps). | [[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin<ref>PMID: 9628483</ref><ref>PMID: 20459678</ref> found in [[1tub]] chain A, length 440. However, the sequence identity is low. 92/372 residues can be aligned with 19% identity (2 gaps), and another 14 residue stretch with 42% identity (no gaps). '''Tests in this section were performed in 2011.''' | ||
====CE example==== | ====CE example==== | ||
*3.2 Å RMSD for 305 residues. The structural | *3.2 Å RMSD for 305 residues. The structural superposition 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. | ||
*12.5% sequence identity within the structural | *12.5% sequence identity within the structural superposition. | ||
*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software | *Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software. | ||
====Dali example==== | ====Dali example==== | ||
*3.2 Å RMSD RIGID | *3.2 Å RMSD RIGID superposition included 299 residues. | ||
*Z-score: 25.5. | *Z-score: 25.5. | ||
*13% sequence identity for the structurally | *13% sequence identity for the structurally superposed regions. | ||
*The structure-based sequence alignment has many gaps. | *The structure-based sequence alignment has many gaps. | ||
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Tested with version 4.01 OS X. | Tested with version 4.01 OS X. | ||
*Magic Fit -- SEQUENCED-BASED: | *Magic Fit -- SEQUENCED-BASED: | ||
**4.4 Å RMSD for 114 | **4.4 Å RMSD for 114 superposed residues. | ||
*Iterative Magic Fit -- Sequence based followed by RMSD minimization: | *Iterative Magic Fit -- Sequence based followed by RMSD minimization: | ||
**1.69 Å RMSD for 159 | **1.69 Å RMSD for 159 superposed residues. | ||
*Explore Domain Alternate Fits -- sequence-independent | *Explore Domain Alternate Fits -- sequence-independent superposition: | ||
**Used option NOT to use selected residues. | **Used option NOT to use selected residues. | ||
**Nevertheless program complained repeatedly that I had not selected residues. | **Nevertheless program complained repeatedly that I had not selected residues. | ||
**Nevertheless program produced an alignment: | **Nevertheless program produced an alignment: | ||
**1.0 Å for 64 | **1.0 Å for 64 superposed residues. | ||
====FATCAT example==== | ====FATCAT example==== | ||
*3.02 Å RMSD RIGID | *3.02 Å RMSD RIGID superposition 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). | ||
*10.2% sequence identity in the structurally | *10.2% sequence identity in the structurally superposed regions. | ||
*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. | ||
*FLEXIBLE | *FLEXIBLE superposition introduced ZERO twists (hinges), so gave the same result as the rigid superposition. | ||
====MAMMOTH example==== | ====MAMMOTH example==== | ||
*4.0 Å (?) with 298 | *4.0 Å (?) with 298 superposed residues (?) (Labeling in results is unclear.) | ||
*Structure-based sequence alignment is displayed. | *Structure-based sequence alignment is displayed. | ||
====PyMOL example==== | ====PyMOL example==== | ||
*Command: super 1fsz////CA, 1tub_a////CA, object=supAB | *Command: super 1fsz////CA, 1tub_a////CA, object=supAB | ||
**4.5 Å RMSD for 197 | **4.5 Å RMSD for 197 superposed residues. | ||
====TM-Align example==== | ====TM-Align example==== | ||
*3.42 Å for 312 | *3.42 Å for 312 superposed residues. | ||
*Structure-based sequence alignment is displayed. | *Structure-based sequence alignment is displayed. | ||
====TopMatch example==== | ====TopMatch example==== | ||
*2.9 Å RMSD. | *2.9 Å RMSD. Superposition includes 275 residues. | ||
*13% sequence identity in the | *13% sequence identity in the superposed regions. | ||
*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was | *Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was superposed with RMSD 2.69 Å, an alternative superposition matching the second domain shows up with 47 residues/RMSD 2.69 Å. | ||
====VAST example==== | ====VAST example==== | ||
* 4.0 Å RMSD for 299 | * 4.0 Å RMSD for 299 superposed residues. | ||
* Expectation value: 10<sup>-16</sup>. | * Expectation value: 10<sup>-16</sup>. | ||
* 11.4% sequence identity in the | * 11.4% sequence identity in the superposed segments. | ||
* '''I could find no way to download the aligned PDB file for visualization in Jmol or RasMol.''' | * '''I could find no way to download the aligned PDB file for visualization in Jmol or RasMol.''' | ||
==References== | ==References== | ||
<references /> | <references /> | ||
