Structure superposition tools: Difference between revisions
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===Examples for Rigid Alignment=== | ===Examples for Rigid Alignment=== | ||
<table align="right" border="1" cellpadding="4" hspace="6" width="350"><tr><td colspan="4" bgcolor="#d0d0d0"> | <table align="right" border="1" cellpadding="4" hspace="6" width="350"><tr><td colspan="4" bgcolor="#d0d0d0"> | ||
Summary for 1fszA vs. 1tubA | Example 1<br>Summary for 1fszA vs. 1tubA | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
Tool</td><td>Residues Aligned</td><td>RMSD, Å</td><td>Unaligned Residues | Tool</td><td>Residues Aligned</td><td>RMSD, Å</td><td>Unaligned Residues | ||
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VAST</td><td>299</td><td>4.0</td><td> | VAST</td><td>299</td><td>4.0</td><td> | ||
</td></tr><tr><td colspan="4" bgcolor="#d0d0d0"> | </td></tr><tr><td colspan="4" bgcolor="#d0d0d0"> | ||
Example 2<br>Mammalian tubulin α vs. β, 1tubA vs. 1tubB: 40% sequence identity. | |||
</td></tr><tr><td> | </td></tr><tr><td> | ||
Tool</td><td>Residues Aligned</td><td>RMSD, Å</td><td>Unaligned Residues | Tool</td><td>Residues Aligned</td><td>RMSD, Å</td><td>Unaligned Residues | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
CE</td><td> | CE</td><td>404</td><td>1.34</td><td>56 | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
Dali</td><td> | Dali</td><td></td><td></td><td> | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
DeepView</td><td> | DeepView</td><td><br></td><td><br></td><td> | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
FATCAT</td><td><b>424</b></td><td><b>1.75</b></td><td> | FATCAT</td><td><b>424</b></td><td><b>1.75</b></td><td>16 | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
PyMOL</td><td> | PyMOL</td><td></td><td></td><td> | ||
</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). | ||
