Structure superposition tools: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Markus Wiederstein, Wayne Decatur, Ronald Ayoub, Joel L. Sussman, Angel Herraez

@@ Line 129: / Line 129: @@
 *Visualization: YES.
 *Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)
-*Offered by RCSB? YES
+*Offered by RCSB? YES, with both options: rigid and flexible.
+*Download result: one pdb file, not using MODEL/ENDMDL delimiters but with the aligned structures labeled as chains A and B. If done at RCSB, download has 2 separate mmCIF files.
 *Special features:
-**Produces a [[morph]] between the two superposed chains (at the link "Interpolating between ...").
+**Produces a [[morph]] between the two superposed chains (at the link "Interpolating between ..."). It is a 10-model PDB file '''with only alpha carbons'''.
 **Offers a RasMol script to color each rigid segment distinctly (separated by twists/hinges).
@@ Line 196: / Line 197: @@
 *Search with uploaded models: YES
 *Color by deviation: ?
-*Special features: ?
+*Special features:
+** Allows specification of restricted regions to superpose.
 ===TM-Align===
@@ Line 216: / Line 218: @@
 *Server: [http://topmatch.services.came.sbg.ac.at/ TopMatch]
-*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>, (2012)<ref name="topmatch3">PMID: 22483118</ref>
+*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>, (2012)<ref name="topmatch3">PMID: 22483118</ref>, (2020)<ref name="topmatch4">PMID: 32479639</ref>
 *Help on server: YES.
 *Does superposition involve sequence comparison? NO.
@@ Line 223: / Line 225: @@
 *Multiple superposition: NO.
 *Structure-based sequence alignment: YES.
-*Structure neighbors (pre-calculated): NO (but see TopSearch).
+*Structure neighbors (pre-calculated): NO (but see [[#TopSearch|TopSearch]]).
 *Pairwise superposition including uploaded models: YES
 *Visualization: YES.
@@ Line 229: / Line 231: @@
 *Offered by RCSB? NO.
 *Special features:
-**Structure superposition of multiprotein complexes.
+**Structure superposition of multichain complexes (of both proteins and nucleic acids).
 **You can download the superposition target PDB file (in a separate file from the query PDB file). A PyMOL script is also available, as is the matrix to transform the target coordinates.
@@ Line 250: / Line 252: @@
 ===VAST===
 *Server: [http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml Vector Alignment Search Tool]
-*Publication (1996)<ref name="topmatch">PMID: 8804824</ref>
+*Publications 1996<ref name="topmatch">PMID: 8804824</ref>, 2014<ref>PMID: 24319143</ref>, 2020<ref>PMID: 32006286</ref>.
 *Help on server: YES.
-*Does alignment involve sequence comparison? UNCLEAR.
+*Does superposition involve sequence comparison? UNCLEAR.
-*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
+*Rigid superposition: ONLY (according to FATCAT<ref name="fatcat" />)
-*Flexible alignment: NO.
+*Flexible superposition: NO.
-*Multiple alignment: NO.
+*Multiple superposition: ?.
 *Structure neighbors (pre-calculated): YES.
-*Pairwise alignment including uploaded models: NO.
+*Pairwise superposition including uploaded models: NO.
 *Visualization: Cn3D. '''There appears to be no way to download the aligned model in PDB format for visualization in Jmol.'''
 *Color by deviation: '''NO''' (at least not in Jmol-compatible form).
@@ Line 266: / Line 268: @@
 ===Structure Navigator of PDB-Japan===
-*Server: [http://www.pdbj.org/doc/help?Structure%20Navigator Structure Navigator]
+*Server: [https://pdbj.org/help/structure-navigator Structure Navigator] '''but server not found in 2021'''.
 *Publication (2007): [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955748/ ASH structure alignment package: Sensitivity and selectivity in domain classification].
 *Help on server: YES.
-*Does alignment involve sequence comparison? Yes, and the sequence alignment for each pair is displayed.
+*Does superposition involve sequence comparison? Yes, and the sequence alignment for each pair is displayed.
-*Rigid alignment: YES.
+*Rigid superposition: YES.
-*Flexible alignment: (Probably not -- unclear.)
+*Flexible superposition: (Probably not -- unclear.)
-*Multiple alignment: ??
+*Multiple superposition: ??
 *Structure neighbors (pre-calculated): ??
 *Pairwise alignment including uploaded models: YES.
@@ Line 280: / Line 282: @@
 *Special features: ??
-==Structural Alignment Software==
+==Structural Superposition Software==
 This section is for stand-alone software packages that do not require a web browser.
-===Calculate Structure Alignment===
-This is a java program (java web start) offered by the U.S. [[PDB]]. At [https://www.rcsb.org/pages/analyze_features#Sequence PDB Sequence & Structure Alignment]. You will then get a form where you can enter two [[PDB codes]] (or upload two PDB files), optionally with a sequence range for each. Alternatively, with the ''Database Search'' option, you can enter a single PDB code (or upload a PDB file), and find structure neighbors. On the right is a link "Align custom files (Launches a Java Web Start application)", which starts the ''Calculate Structure Alignment'' java software. This package offers java implementations of the CE and FATCAT (you can choose '''rigid''' or '''flexible''') algorithms (see above).
-* Pairwise Comparison: displays the alignment in Jmol, and a sequence alignment (presumably structure-based).
-* Database Search: I got no results after clicking "Align" for either jCE or jFATCAT - rigid. These options did not appear to be working. [[User:Eric Martz|Eric Martz]] 16:28, 4 October 2010 (IST)
-* Help is minimal and results are not clearly labeled.
 ===DeepView = Swiss-PDBViewer===
 *Download site: [http://www.expasy.org/spdbv/ DeepView Swiss-PdbViewer].
+*[https://spdbv.unil.ch/superpos_tut.html Tutorial on superposition using DeepView].
 *Publications (1997, 1999)<ref>PMID: 9504803</ref><ref>PMID: 10470037</ref>
-*Version 4.01 released in 2008.
+*Version 4.11 released in 2019; works on Windows and macOS 10.5-10.14.
-*'''Caution''': This program often reports the wrong number of alpha carbons aligned, typically reporting twice or four-times the actual number. In order to get the correct count, use the Fit menu, Calculate RMS, or observe the number of residues selected in each layer.
+*'''Caution''': This program may report the wrong number of alpha carbons superposed, typically reporting twice or four-times the actual number. In order to get the correct count, use the Fit menu, Calculate RMS, or observe the number of residues selected in each layer.
 *Help: YES.
-* Fit, Magic Fit does a '''sequence-based''' structural alignment.
+* Fit, Magic Fit does a '''sequence-based''' structural superposition.
-* Fit, Iterative Magic Fit starts with a sequence-based structural alignment, then does further structural alignment, minimizing the RMSD.
+* Fit, Iterative Magic Fit starts with a sequence-based structural superposition, then does further structural superposition over a smaller number of residues, further minimizing the RMSD.
-* Fit, Explore Domain Alternate Fits: does a '''sequence-independent''' structural alignment.
+* Fit, Explore Domain Alternate Fits: does a '''sequence-independent''' structural superposition.
 * Magic Fit and Iterative Magic Fit can '''align multiple chains in each model''' and can '''align DNA chains''' as well as protein chains.
 * Color, RMS: colors the target structure by deviation.
@@ Line 304: / Line 300: @@
 ===Jmol===
-Since this article was researched and written in 2010, a new ''compare'' command was implemented in Jmol that does structural alignment. See
+See
-* [[Superposition with jmol]] which explains the method in Jmol.
+* [[Jmol/Superposition]] which explains the method in Jmol.
 * [[Samatey/1#Comparison]] which shows an animation of alignment performed by Jmol.
 * [[Samatey/2#Comparison_with_Thermotoga]] which has buttons that animate the alignments of different domains.
@@ Line 312: / Line 308: @@
 ===PyMOL===
 *Download site: [http://www.pymol.org/ PyMOL.Org]
-*The ''super'' command does structural alignment.
+*The ''super'' command does structural superposition.
 *Color by RMSD: YES [http://www.pymolwiki.org/index.php/ColorByRMSD example].
 ===UCSF Chimera===
-*Download site: [https://www.cgl.ucsf.edu/chimera/download.html]
+*Download site: [https://www.cgl.ucsf.edu/chimera/download.html www.cgl.ucsf.edu/chimera/download.html]
-*The ''matchmaker'' command does structural alignment, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]. Or use "match" to specify exact atom pairs, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]
+*The ''matchmaker'' command does structural superposition, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]. Or use "match" to specify exact atom pairs, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]
 *Color by RMSD: YES [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012379.html steps outlined under '(4)'] or [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-April/007393.html Under '(A)' here]
 ===TopMatch===
@@ Line 331: / Line 326: @@
 ===Example Requiring Flexibility===
-'''This example requires flexibility for a good alignment''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.
+Tests performed in 2011. '''This example requires flexibility for a good superposition''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.
 *CE:
 **4.8 &Aring; RMSD.
@@ Line 349: / Line 344: @@
 Example 1<br>Summary for 1fszA vs. 1tubA
 </td></tr><tr><td>
-Tool</td><td>Residues Aligned</td><td>RMSD, &Aring;</td><td>Unaligned Residues /Total
+Tool</td><td>Residues Superposed</td><td>RMSD, &Aring;</td><td>Residues Not Superposed/Total
 </td></tr><tr><td>
 CE</td><td>305</td><td>3.2</td><td>96/401
@@ Line 371: / Line 366: @@
 Example 2<br>Mammalian tubulin &alpha; vs. &beta;, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.
 </td></tr><tr><td>
-Tool</td><td>Residues Aligned</td><td>RMSD, &Aring;</td><td>Unaligned Residues
+Tool</td><td>Residues Superposed</td><td>RMSD, &Aring;</td><td>Residues Not Superposed
 </td></tr><tr><td>
 CE</td><td>404</td><td>1.34</td><td>56/"460"(?)
@@ Line 384: / Line 379: @@
 <tr><td>Topmatch</td><td>416</td><td>1.68
 </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====
-*3.2 &Aring; 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 &Aring; 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.
-*12.5% sequence identity within the structural alignment.
+*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 (see above).
+*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software.
 ====Dali example====
-*3.2 &Aring; RMSD RIGID alignment included 299 residues.
+*3.2 &Aring; RMSD RIGID superposition included 299 residues.
 *Z-score: 25.5.
-*13% sequence identity for the structurally aligned regions.
+*13% sequence identity for the structurally superposed regions.
 *The structure-based sequence alignment has many gaps.
@@ Line 400: / Line 395: @@
 Tested with version 4.01 OS X.
 *Magic Fit -- SEQUENCED-BASED:
-**4.4 &Aring; RMSD for 114 aligned residues.
+**4.4 &Aring; RMSD for 114 superposed residues.
 *Iterative Magic Fit -- Sequence based followed by RMSD minimization:
-**1.69 &Aring; RMSD for 159 aligned residues.
+**1.69 &Aring; RMSD for 159 superposed residues.
-*Explore Domain Alternate Fits -- sequence-independent alignment:
+*Explore Domain Alternate Fits -- sequence-independent superposition:
 **Used option NOT to use selected residues.
 **Nevertheless program complained repeatedly that I had not selected residues.
 **Nevertheless program produced an alignment:
-**1.0 &Aring; for 64 aligned residues.
+**1.0 &Aring; for 64 superposed residues.
 ====FATCAT example====
-*3.02 &Aring; RMSD RIGID alignment includes 298 residues.
+*3.02 &Aring; RMSD RIGID superposition includes 298 residues.
 *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 aligned regions.
+*10.2% sequence identity in the structurally superposed regions.
 *The structure-based sequence alignment has many gaps, looking similar to that generated by CE.
-*FLEXIBLE alignment introduced ZERO twists (hinges), so gave the same result as the rigid alignment.
+*FLEXIBLE superposition introduced ZERO twists (hinges), so gave the same result as the rigid superposition.
 ====MAMMOTH example====
-*4.0 &Aring; (?) with 298 aligned residues (?) (Labeling in results is unclear.)
+*4.0 &Aring; (?) with 298 superposed residues (?) (Labeling in results is unclear.)
 *Structure-based sequence alignment is displayed.
 ====PyMOL example====
 *Command: super 1fsz////CA, 1tub_a////CA, object=supAB
-**4.5 &Aring; RMSD for 197 aligned residues.
+**4.5 &Aring; RMSD for 197 superposed residues.
 ====TM-Align example====
-*3.42 &Aring; for 312 aligned residues.
+*3.42 &Aring; for 312 superposed residues.
 *Structure-based sequence alignment is displayed.
 ====TopMatch example====
-*2.9 &Aring; RMSD. Alignment includes 275 residues.
+*2.9 &Aring; RMSD. Superposition includes 275 residues.
-*13% sequence identity in the aligned regions.
+*13% sequence identity in the superposed regions.
-*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was aligned with RMSD 2.69 &Aring;, an alternative alignment matching the second domain shows up with 47 residues/RMSD 2.69 &Aring;.
+*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was superposed with RMSD 2.69 &Aring;, an alternative superposition matching the second domain shows up with 47 residues/RMSD 2.69 &Aring;.
 ====VAST example====
-* 4.0 &Aring; RMSD for 299 aligned residues.
+* 4.0 &Aring; RMSD for 299 superposed residues.
 * Expectation value: 10<sup>-16</sup>.
-* 11.4% sequence identity in the aligned segments.
+* 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.'''
 ==References==
 <references />