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''Structural superposition'' refers to the optimal superposition, yielding the closest fit, in three dimensions, between two or more molecular models. It is sometimes called ''structural alignment'', but that term more often denotes a sequence alignment guide by a structural superposition. In the case of proteins, structural superposition is often performed without reference to the sequences of the proteins. When the models superpose closely, it suggests evolutionary and functional relationships that may not be discernable from sequence comparisions<ref>PMID: 10686110</ref>.  
''Structure superposition'' refers to the optimal superposition, yielding the closest fit in three dimensions, between two or more molecular models. It is sometimes called ''structure alignment'', but that term is easily confused with a sequence alignment guided by a structure superposition. In the case of proteins, structure superposition is often performed without reference to the sequences of the proteins. When the models superpose closely, it suggests evolutionary and functional relationships that may not be discernable from sequence comparisions<ref>PMID: 10686110</ref>.  


The purpose of this article is to help in choosing a server or software package for performing structural superposition. Characteristics of structural superposition servers and software packages are listed, along with results of testing with a few examples.
The purpose of this article is to help in choosing a server or software package for performing structure superposition. Characteristics of structure superposition servers and software packages are listed, along with results of testing with a few examples.


There are two common applications of structural superposition servers:
There are two common applications of structure superposition servers:
# '''Pairwise superposition'''. All servers listed below enable you to upload two 3D models (or specify them from the [[PDB]]) and generate a structural superposition.
# '''Pairwise superposition'''. All servers listed below enable you to upload two 3D models (or specify them from the [[PDB]]) and generate a structure superposition.
# '''Structure neighbors'''. Some servers (notably [[#Dali|Dali]],  [[#FATCAT|FATCAT]], [[#VAST|VAST]] and [[#TopSearch|TopSearch]]) enable you to upload one 3D model (or specify one in the [[PDB]]) and generate a list of the closest structures in the [[PDB]], based on pairwise structural superpositions between your query structure versus each structure in the [[PDB]].
# '''Structure neighbors'''. Some servers (notably [[#Dali|Dali]],  [[#FATCAT|FATCAT]], [[#VAST|VAST]] and [[#TopSearch|TopSearch]]) enable you to upload one 3D model (or specify one in the [[PDB]]) and generate a list of the closest structures in the [[PDB]], based on pairwise structure superpositions between your query structure versus each structure in the [[PDB]].


Wikipedia offers a [http://en.wikipedia.org/wiki/Structural_alignment_software list of structural superposition software packages] and an overview of [http://en.wikipedia.org/wiki/Structural_alignment structural superposition]. Hasegawa and Holm reviewed structural superposition methods in 2009<ref>PMID: 19481444</ref>.
Wikipedia offers a [http://en.wikipedia.org/wiki/Structural_alignment_software list of structure superposition software packages] and an overview of [http://en.wikipedia.org/wiki/Structural_alignment structure superposition]. Hasegawa and Holm reviewed structure superposition methods in 2009<ref>PMID: 19481444</ref>.


==Evaluating Structural Superpositions==
==Evaluating Structure Superpositions==
The structural differences between two optimally superposed models are usually measured as the [http://en.wikipedia.org/wiki/RMSD Root Mean Square Deviation] ('''RMSD''') between the superposed alpha-carbon positions (excluding deviations from the non-superposed positions). To provide a frame of reference for RMSD values, note that up to 0.5 Å RMSD of alpha carbons occurs in independent determinations of the same protein<ref name="chothia86">PMID: 3709526</ref>. Crystallographic models of proteins with about 50% sequence identity differ by about 1 &Aring; RMSD<ref name="chothia86" /><ref name="3dcrunch">PMID: 10865955</ref>. Deviations can be much larger for models determined by [[NMR]]<ref name="3dcrunch" />.
The structural differences between two optimally superposed models are usually measured as the [http://en.wikipedia.org/wiki/RMSD Root Mean Square Deviation] ('''RMSD''') between the superposed alpha-carbon positions (excluding deviations from the non-superposed positions). To provide a frame of reference for RMSD values, note that up to 0.5 Å RMSD of alpha carbons occurs in independent determinations of the same protein<ref name="chothia86">PMID: 3709526</ref>. Crystallographic models of proteins with about 50% sequence identity differ by about 1 &Aring; RMSD<ref name="chothia86" /><ref name="3dcrunch">PMID: 10865955</ref>. Deviations can be much larger for models determined by [[NMR]]<ref name="3dcrunch" />.


The statistical significance of a structural superposition, relative to a superposition of random sequence-nonredundant structures in the [[PDB]], is usually measured with a '''[http://en.wikipedia.org/wiki/Standard_score z-score]'''. The z-score is the distance, in standard deviations, between the observed alignment RMSD and the mean RMSD for random pairs of the same length, with the same or fewer gaps. Z-scores less than 2 are considered to lack statistical significance.
The statistical significance of a structure superposition, relative to a superposition of random sequence-nonredundant structures in the [[PDB]], is usually measured with a '''[http://en.wikipedia.org/wiki/Standard_score z-score]'''. The z-score is the distance, in standard deviations, between the observed superposition RMSD and the mean RMSD for random pairs of the same length, with the same or fewer gaps. Z-scores less than 2 are considered to lack statistical significance.


When the models being compared have substantial differences, and especially if they have multiple domains, different estimates of the closenss of fit have been employed, notably in [[CASP]]. One of these is the ''global distance test total score'', or [[Calculating_GDT_TS|GDT_TS]]. See also [[Theoretical models]].
When the models being compared have substantial differences, and especially if they have multiple domains, more tolerant estimates of the closenss of fit have been employed, notably in [[CASP]]. One of these is the ''global distance test total score'', or [[Calculating_GDT_TS|GDT_TS]]. See also [[Theoretical models]].


==Visualizing Structural Alignments==
==Visualizing Structure Superpositions==
<applet size='400' frame='true' align='right' caption='Structural alignment of [[1fsz]] with [[1tub]].'
<applet size='400' frame='true' align='right' caption='Structural alignment of [[1fsz]] with [[1tub]].'
scene='Structural_alignment_tools/Dali_chains_ab_water/1' />
scene='Structural_alignment_tools/Dali_chains_ab_water/1' />
Structural alignments are usually visualized as the superimposed backbone traces of the aligned models. The example at right shows the bacterial cell division protein <font color="#d80000"><b>FtsZ</b></font> ([[1fsz]]:A) aligned by [[#Dali|Dali]] with <!--e0b000--><font color="#d0a000"><b>mammalian tubulin</b></font> ([[1tub]]:A). Sequence identity in the structurally aligned regions is about 13%.
Structure superpositions are usually visualized as the superposed backbone traces of the models. The example at right shows the bacterial cell division protein <font color="#d80000"><b>FtsZ</b></font> ([[1fsz]]:A) superposed by [[#Dali|Dali]] with <!--e0b000--><font color="#d0a000"><b>mammalian tubulin</b></font> ([[1tub]]:A). Sequence identity in the superposed regions is about 13%.
*The non-aligned segments are white in the query (<font color="#d80000"><b>FtsZ</b></font>) and thin in the target (<font color="#d0a000"><b>tubulin</b></font>). This scene is available in [[#Dali|Dali]] except that the target color has been changed to make it more distinct from the red query. (<scene name='Structural_alignment_tools/Dali_chains_ab_water/1'>Restore initial scene</scene>.)
*The non-superposed segments are white in the query (<font color="#d80000"><b>FtsZ</b></font>) and thin in the target (<font color="#d0a000"><b>tubulin</b></font>). This scene is available in [[#Dali|Dali]] except that the target color has been changed to make it more distinct from the red query. (<scene name='Structural_alignment_tools/Dali_chains_ab_water/1'>Restore initial scene</scene>.)
*Because the alignment is about 300 residues long (and the protein chains are longer), it is hard to see details of this alignment in the complexity. Buttons below show 50-residue segments of the query (<font color="#d80000"><b>FtsZ</b></font>) and backbone for target  (<font color="#d0a000"><b>tubulin</b></font>) where the target &alpha; carbons are within 3.5 &Aring;. (The RMSD for this [[#Dali|Dali]] alignment is 3.2 &Aring;.)
*Because the superposition is about 300 residues long (and the protein chains are longer), it is hard to see details of this superposition in the complexity. Buttons below show 50-residue segments of the query (<font color="#d80000"><b>FtsZ</b></font>) and backbone for target  (<font color="#d0a000"><b>tubulin</b></font>) where the target &alpha; carbons are within 3.5 &Aring;. (The RMSD for this [[#Dali|Dali]] superposition is 3.2 &Aring;.)
<jmol>
<jmol>
<jmolButton>
<jmolButton>
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</jmolButton>
</jmolButton>
</jmol>
</jmol>
* This <scene name='Structural_alignment_tools/Morph_1fsz_1tub_a_fatcat/1'>morph of the alignment</scene> was generated by [[#FATCAT|FATCAT]], which reported 3.02 &Aring; RMSD for 298 structurally aligned residues, and 10.2% sequence identity for the structurally aligned residues. The morph shows the 334-residue sequence of the query (FtsZ) changing from the query conformation to the conformation of the aligned target (tubulin). It does not show the non-aligned loops of tubulin that can be seen as thin backbone traces in the initial scene above. The morph makes it easy to see that the core fold is stable, while the larger changes occur in surface loops.
* This <scene name='Structural_alignment_tools/Morph_1fsz_1tub_a_fatcat/1'>morph of the superposition</scene> was generated by [[#FATCAT|FATCAT]], which reported 3.02 &Aring; RMSD for 298 superposed residues, and 10.2% sequence identity for the superposed residues. The morph shows the 334-residue sequence of the query (FtsZ) changing from the query conformation to the conformation of the superposed target (tubulin). It does not show the non-superposed loops of tubulin that can be seen as thin backbone traces in the initial scene above. The morph makes it easy to see that the core fold is stable, while the larger changes occur in surface loops.


It is very helpful to color the target alpha carbons by deviation ("RMSD") from the query model: red indicates large deviations (poor alignment) while blue indicates small deviations (good alignment), with white indicating average alignment. The stand-alone programs [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] and [[#PyMOL|PyMOL]] color alignments by RMSD but the results cannot be easily exported to Jmol. Surprisingly, none of the servers listed below color their alignments by deviation. Unfortunately, I found NO way to color the alignment by RMSD in Jmol.
It is very helpful to color the target alpha carbons by deviation ("RMSD") from the query model: red indicates large deviations (poor superposition) while blue indicates small deviations (close superposition), with white indicating average superposition. The stand-alone programs [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] and [[#PyMOL|PyMOL]] color superpositions by RMSD but the results cannot be easily exported to Jmol. Surprisingly, none of the servers listed below color their superpositions by deviation, except [[#Dali|Dali]]. Unfortunately, there is NO built-in way to color the superposition by RMSD in Jmol.


==Conclusions==
==Conclusions==
===Protein structural alignment===
===Protein structural superposition===
There are several well-documented, easy to use servers and software packages that do an excellent job of sequence-independent structural alignment, described below.  They include
There are several well-documented, easy to use servers and software packages that do an excellent job of sequence-independent structure superposition, described below.  They include
* [[#CE|CE]] rigid alignment only (see Note below).
* [[#CE|CE]] rigid superposition only.
* [[#Dali|Dali]] rigid alignment only. Jmol. Colors by ''structure conservation'' distinguishing aligned from non-aligned segments.
* [[#Dali|Dali]] rigid superposition only. Jmol. Colors by ''structure conservation'' distinguishing closely superposed from poorly superposed segments.
* [[#FATCAT|FATCAT]] '''flexible''' and rigid alignment. Jmol. Generates '''morph''' of alignment.
* [[#FATCAT|FATCAT]] '''flexible''' and rigid superposition. Jmol. Generates '''morph''' of alignment.
* [[#TopMatch|TopMatch]]
* [[#TopMatch|TopMatch]]
Note: Although the CE server appears not to be well maintained, the CE algorithms can be used at [http://www.pdb.org pdb.org] either directly in their website, or via their java web start application (see instructions below under [[#Calculate Structure Alignment|Calculate Structure Alignment]]). Both of the latter methods include visualization in Jmol (not available at the CE website).


If you want automated selection of a small subdomain with the best possible alignment, try [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]]'s ''Explore Domain Alternate Fits'' or ''Iterative Magic Fit'' (see results in the [[#DeepView = Swiss-PDBViewer example|DeepView = Swiss-PDBViewer example]]).
If you want automated selection of a small subdomain with the best possible superposition, try [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]]'s ''Explore Domain Alternate Fits'' or ''Iterative Magic Fit'' (see results in the [[#DeepView = Swiss-PDBViewer example|DeepView = Swiss-PDBViewer example]]).


===DNA structural alignment===
===DNA structure superposition===
None of the above servers does structural alignment of DNA, but  [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] does (''Iterative Magic Fit'').
None of the above servers does structure superposition of DNA, but  [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] does (''Iterative Magic Fit'').


===Multiple chain structural alignment===
===Multiple chain structure superposition===
====Multiple chains in each of two models====
====Multiple chains in each of two models====
CE and FATCAT align only one chain at a time. DaliLite appears to align multiple chains, although the output is confusing and not clearly labeled.  [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] can align multiple chains, including both protein and DNA chains in a single alignment (''Iterative Magic Fit'').  [[#TopMatch|TopMatch]] and [[#TopSearch|TopSearch]] can also align multichain protein assemblies.
CE and FATCAT superpose only one chain at a time. DaliLite appears to superpose multiple chains, although the output is confusing and not clearly labeled.  [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] can superpose multiple chains, including both protein and DNA chains in a single superposition (''Iterative Magic Fit'').  [[#TopMatch|TopMatch]] and [[#TopSearch|TopSearch]] can also superpose multichain protein assemblies.


====One chain vs. many other chains====
====One chain vs. many other chains====
Line 85: Line 84:


===CE===
===CE===
The ''Combinatorial Extension'' structural alignment server. See the [http://en.wikipedia.org/wiki/Structural_alignment#Combinatorial_extension explanation of CE methodology at Wikipedia].
The ''Combinatorial Extension'' method. See the [http://en.wikipedia.org/wiki/Structural_alignment#Combinatorial_extension explanation of CE methodology at Wikipedia].
*Server: [http://cl.sdsc.edu/ CE Home Page].
*Server: Use [http://rcsb.org rcsb.org] At the main page, click on Analyze, then on Pairwise Structure Alignment.<!--[http://cl.sdsc.edu/ CE Home Page].-->
*Publication (1998)<ref>PMID: 9796821</ref>
*Publication (1998)<ref>PMID: 9796821</ref>
*'''N.B. Database of structure neighbors has not been updated since 2004. Java applet for viewing results is not working in Sept. 2010. Finding structure neighbors from the entire PDB database ("ALL") appears to have been broken since 2001.'''
<!--*'''N.B. Database of structure neighbors has not been updated since 2004. Java applet for viewing results is not working in Sept. 2010. Finding structure neighbors from the entire PDB database ("ALL") appears to have been broken since 2001.'''-->
*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
*Align DNA? NO.
*Align DNA? NO.
*Align multiple protein chains? NO. Aligns one pair of chains at a time.
*Align multiple protein chains? NO. Aligns one pair of chains at a time.
*Structure-based sequence alignment: YES.
*Structure-based sequence alignment: YES.
*Visualization: does not appear to work on the website, but visualization in Jmol works when the jCE option is used in the ''Calculate Structural Alignment'' java software (see below).
*Visualization: Mol*.
*Offered by RCSB? YES.
*Offered by RCSB? YES.


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"Dali does not optimize RMSD, it matches contacts" (Dali Tutorial, section 4.4.2). See the [http://en.wikipedia.org/wiki/Structural_alignment#DALI explanation of Dali's methods at Wikipedia].
"Dali does not optimize RMSD, it matches contacts" (Dali Tutorial, section 4.4.2). See the [http://en.wikipedia.org/wiki/Structural_alignment#DALI explanation of Dali's methods at Wikipedia].
*Server: [http://ekhidna.biocenter.helsinki.fi/dali Dali Server]  
*Server: [http://ekhidna.biocenter.helsinki.fi/dali Dali Server]  
*Publication (2010)<ref name="dali">PMID: 20457744</ref>  
*Publication 2010<ref name="dali">PMID: 20457744</ref>, 2020<ref>PMID: 32006276</ref>.
*Help on server: YES, including an extensive ''Dali Tutorial'' (PDF) with many screenshots. This refers to a ''Dali Manual'' which I could not find.
*Help on server: YES, including an extensive ''Dali Tutorial'' (PDF) with many screenshots.
*Does the structural alignment involve sequence comparison? UNCLEAR.
*Does the structure superposition involve sequence comparison? UNCLEAR.
*Rigid alignment: YES (section 4.4.2 of the Dali Tutorial). ONLY (according to FATCAT<ref name="fatcat" />)
*Rigid superposition: YES (section 4.4.2 of the Dali Tutorial). ONLY (according to FATCAT<ref name="fatcat" />)
*Flexible alignment: NO.
*Flexible superposition: NO.
*Structure neighbors (pre-calculated): YES
*Structure neighbors (pre-calculated): YES
*Align DNA? NO.
*Superpose DNA? NO.
*Align multiple protein chains? YES? (Results are inadequately labeled and confusing.)
*Superpose multiple protein chains? YES? (Results are inadequately labeled and confusing.)
*Pairwise alignment including uploaded models: YES
*Pairwise superposition including uploaded models: YES
*Ligands: KEPT.
*Ligands: KEPT.
*Visualization: Jmol.
*Visualization: YES. No color key on the visualization page.
*Color by deviation: '''NO'''.
*Color by deviation: YES ("Structure Conservation").
*Offered by RCSB? NO.
*Offered by RCSB? NO.
*Special features:
*Special features:
**Colors 3D visualization in Jmol by sequence conservation, calculated from the checked models.
**Colors 3D visualization by sequence conservation, calculated from the checked models. No color key on the visualization page.
**Colors 3D visualization in Jmol by structure conservation (red for aligned portions, white for unaligned portions).


===FATCAT===
===FATCAT===
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*Publication (2003)<ref name="fatcat">PMID: 14534198</ref> "... the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges."
*Publication (2003)<ref name="fatcat">PMID: 14534198</ref> "... the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges."
*Help on server: YES with snapshots; some context-sensitive help.
*Help on server: YES with snapshots; some context-sensitive help.
*Does alignment involve sequence comparison? UNCLEAR.
*Does superposition involve sequence comparison? UNCLEAR.
*Rigid alignment: YES (optional)
*Rigid superposition: YES (optional)
*Flexible alignment: YES (optional)
*Flexible superposition: YES (optional)
*Structure neighbors (pre-calculated): YES
*Structure neighbors (pre-calculated): YES
*Pairwise alignment including uploaded models: YES
*Pairwise superposition including uploaded models: YES
*Align DNA: NO.
*Superpose DNA: NO.
*Align multiple protein chains: NO. Aligns a single pair of chains at a time.
*Superpose multiple protein chains: NO. Aligns a single pair of chains at a time.
*Structure-based sequence alignment: YES
*Structure-based sequence alignment: YES
*Visualization: Jmol or Chime. See ''Special features''.
*Visualization: YES.
*Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)
*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:
*Special features:
**Produces a morph between the two aligned 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).
**Offers a RasMol script to color each rigid segment distinctly (separated by twists/hinges).


Notes from the publication: With 10 "difficult examples"<ref>Fischer,D., Elofsson,A., Rice,D. and Eisenberg,D. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In Pacific Symposium on Biocomputing. pp. 300–318.</ref> FATCAT produced results comparable (length, RMSD) to the rigid alignment servers DALI, VAST, CE with no twists in 8 cases. This shows that FATCAT is not biased to introduce twists (hinges). Hinges were introduced in two of the difficult cases, producing arguably better alignments. In a comparison with ''FlexProt''<ref>PMID: 12112693</ref>, FATCAT obtained similar RMSD's and aligned lengths with fewer twists (hinges).
Notes from the publication: With 10 "difficult examples"<ref>Fischer,D., Elofsson,A., Rice,D. and Eisenberg,D. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In Pacific Symposium on Biocomputing. pp. 300–318.</ref> FATCAT produced results comparable (length, RMSD) to the rigid superposition servers DALI, VAST, CE with no twists in 8 cases. This shows that FATCAT is not biased to introduce twists (hinges). Hinges were introduced in two of the difficult cases, producing arguably better superpositions. In a comparison with ''FlexProt''<ref>PMID: 12112693</ref>, FATCAT obtained similar RMSD's and aligned lengths with fewer twists (hinges).


===FlexProt===
===FlexProt===
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*Server: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt].
*Server: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt].
*Publication (2002)<ref>PMID: 12112693</ref>
*Publication (2002)<ref>PMID: 12112693</ref>
*Rigid alignment: YES (Results include alignment for 0 hinges, but only a well-aligning subset of residues are aligned.)
*Rigid superposition: YES (Results include alignment for 0 hinges, but only a well-aligning subset of residues are aligned.)
*Flexible alignment: YES (Results are given for various numbers of hinges.)
*Flexible superposition: YES (Results are given for various numbers of hinges.)
*Visualization: '''NONE''' (You can download PDB files.)
*Visualization: '''NONE''' (You can download PDB files.)
*Ligands: '''Discarded'''.
*Ligands: '''Discarded'''.
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*Publication (2002)<ref name="mammoth">PMID: 12381844</ref>
*Publication (2002)<ref name="mammoth">PMID: 12381844</ref>
*Help on server: Little or none.
*Help on server: Little or none.
*Does alignment involve sequence comparison? NO: They state that this is a "sequence-independent structural alignment".
*Does superposition involve sequence comparison? NO: They state that this is a "sequence-independent structural alignment".
*Rigid alignment: YES.
*Rigid superposition: YES.
*Flexible alignment: NO.
*Flexible superposition: NO.
*Multiple alignment: YES.
*Multiple superposition: YES.
*Structure neighbors (pre-calculated): NO.
*Structure neighbors (pre-calculated): NO.
*Pairwise alignment including uploaded models: YES
*Pairwise superposition including uploaded models: YES
*Visualization: None (you can download a PDB file and a RasMol script. '''PDB file lacks MODEL/ENDMDL delimiters. PDB file has no chain names. There is a PDB file with chains A and B in the downloadable file ''rasmol.tcl'' but this is not a Jmol-ready file.''')
*Visualization: None (you can download a PDB file and a RasMol script. '''PDB file lacks MODEL/ENDMDL delimiters. PDB file has no chain names. There is a PDB file with chains A and B in the downloadable file ''rasmol.tcl'' but this is not a Jmol-ready file.''')
*Color by deviation: '''NO'''.  
*Color by deviation: '''NO'''.  
*Offered by RCSB? YES
*Offered by RCSB? NO.
 
===MATRAS===


*Server: [http://strcomp.protein.osaka-u.ac.jp/matras/ MATRAS]


:This server came to my attention after this article was written. I hope to evaluate it in the future -- or someone else is encouraged to do so. [[User:Eric Martz|Eric Martz]] 00:30, 7 July 2011 (IDT)


===RUPEE===
===RUPEE===
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*Help on server: YES.
*Help on server: YES.
*Structure neighbors (pre-calculated): NO.
*Structure neighbors (pre-calculated): NO.
*Does alignment involve sequence comparison? NO.
*Does superposition involve sequence comparison? NO.
*Rigid alignment: YES.
*Rigid superposition: YES.
*Flexible alignment: NO.
*Flexible superposition: NO.
*Multiple alignment: NO.
*Multiple superposition: NO.
*Structure-based sequence alignment: YES  
*Structure-based sequence alignment: YES  
*Search with uploaded models: YES
*Search with uploaded models: YES
*Visualization: 3Dmol.js
*Visualization: YES.
*Color by deviation: NO.  
*Color by deviation: NO.  
*Special features:
*Special features:
**Purely geometric structure search with no dependence on sequence.
**Purely geometric structure search with no dependence on sequence.
**For each result, provides a 3d structure alignment, a sequence alignment, and a downloadable PDB alignment file.
**For each result, provides a 3d structure superposition, a sequence alignment, and a downloadable PDB superposition file.
**Provide results even for uploaded PDB files with very low resemblance to existing structures. Therefore, is suitable for testing the output of protein structure prediction algorithms.  
**Provides results even for uploaded PDB files with very low resemblance to existing structures. Therefore, is suitable for testing the output of protein structure prediction algorithms.


===SuperPose===
===SuperPose===
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*Structure neighbors (pre-calculated): ?
*Structure neighbors (pre-calculated): ?
*Visualization: ?
*Visualization: ?
*Does alignment involve sequence comparison: ?  
*Does superposition involve sequence comparison: ?  
*Rigid alignment: ?
*Rigid superposition: ?
*Flexible alignment: ?
*Flexible superposition: ?
*Multiple alignment: YES.
*Multiple superposition: YES.
*Structure-based sequence alignment: ?
*Structure-based sequence alignment: ?
*Search with uploaded models: YES
*Search with uploaded models: YES
*Color by deviation: ?
*Color by deviation: ?
*Special features: ?
*Special features:
** Allows specification of restricted regions to superpose.


===TM-Align===
===TM-Align===
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*Publication (2005)<ref name="mammoth">PMID: 15849316</ref>
*Publication (2005)<ref name="mammoth">PMID: 15849316</ref>
*Help on server: A little.
*Help on server: A little.
*Does alignment involve sequence comparison? UNCLEAR.
*Does superposition involve sequence comparison? UNCLEAR.
*Rigid alignment: YES.
*Rigid superposition: YES.
*Flexible alignment: NO.
*Flexible superposition: NO.
*Multiple alignment: You can download the software to run on linux.
*Multiple superposition: You can download the software to run on linux.
*Structure neighbors (pre-calculated): NO.
*Structure neighbors (pre-calculated): NO.
*Pairwise alignment including uploaded models: YES
*Pairwise superposition including uploaded models: YES
*Visualization: Yes (You can right click on the visualization in JSmol and save the file shown. Also, you can download a script for RasMol that contains PDB coordinates. '''PDB file lacks MODEL/ENDMDL delimiters. PDB file has no chain names. File does not run as a script in Jmol due to REMARK lines that are not legal Jmol commands.''' You can open the downloaded file directly in PyMOL.)  
*Visualization: Yes (You can right click on the visualization in JSmol and save the file shown. Also, you can download a script for RasMol that contains PDB coordinates. '''PDB file lacks MODEL/ENDMDL delimiters. PDB file has no chain names. File does not run as a script in Jmol due to REMARK lines that are not legal Jmol commands.''' You can open the downloaded file directly in PyMOL.)  
*Color by deviation: '''NO'''.  
*Color by deviation: '''NO'''.  
*Offered by RCSB? YES
*Offered by RCSB? YES.


===TopMatch===
===TopMatch===


*Server: [http://topmatch.services.came.sbg.ac.at/ TopMatch]  
*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.
*Help on server: YES.
*Does alignment involve sequence comparison? NO.
*Does superposition involve sequence comparison? NO.
*Rigid alignment: YES.
*Rigid superposition: YES.
*Flexible alignment: NO.
*Flexible superposition: NO.
*Multiple alignment: NO.
*Multiple superposition: NO.
*Structure-based sequence alignment: YES.
*Structure-based sequence alignment: YES.
*Structure neighbors (pre-calculated): NO (but see TopSearch).
*Structure neighbors (pre-calculated): NO (but see [[#TopSearch|TopSearch]]).
*Pairwise alignment including uploaded models: YES
*Pairwise superposition including uploaded models: YES
*Visualization: JSmol.  
*Visualization: YES.  
*Color by deviation: NO.  
*Color by deviation: NO.  
*Offered by RCSB? YES
*Offered by RCSB? NO.
*Special features:
*Special features:
**Structure alignment of multiprotein complexes.
**Structure superposition of multichain complexes (of both proteins and nucleic acids).
**You can download the aligned 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.
**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.


===TopSearch===
===TopSearch===
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*Help on server: YES.
*Help on server: YES.
*Structure neighbors (pre-calculated): YES.
*Structure neighbors (pre-calculated): YES.
*Does alignment involve sequence comparison? NO.
*Does superposition involve sequence comparison? NO.
*Rigid alignment: YES.
*Rigid superposition: YES.
*Flexible alignment: NO.
*Flexible superposition: NO.
*Multiple alignment: NO.
*Multiple superposition: NO.
*Structure-based sequence alignment: YES (indirectly, via link to [[#TopMatch|TopMatch]]).
*Structure-based sequence alignment: YES (indirectly, via link to [[#TopMatch|TopMatch]]).
*Search with uploaded models: YES
*Search with uploaded models: YES
*Visualization: JSmol.  
*Visualization: YES.  
*Color by deviation: NO.  
*Color by deviation: NO.  
*Special features: Structure search of multichain protein complexes.
*Special features: Structure search of multichain protein complexes.
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===VAST===
===VAST===
*Server: [http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml Vector Alignment Search Tool]  
*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.
*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.
*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.'''
*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).  
*Color by deviation: '''NO''' (at least not in Jmol-compatible form).  
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===Structure Navigator of PDB-Japan===
===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].
*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.
*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): ??
*Structure neighbors (pre-calculated): ??
*Pairwise alignment including uploaded models: YES.
*Pairwise alignment including uploaded models: YES.
Line 286: Line 282:
*Special features: ??
*Special features: ??


==Structural Alignment Software==
==Structural Superposition Software==
This section is for stand-alone software packages that do not require a web browser.
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===
===DeepView = Swiss-PDBViewer===
*Download site: [http://www.expasy.org/spdbv/ 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>
*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.
*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.
* 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.
* Color, RMS: colors the target structure by deviation.
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===Jmol===
===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/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.
* [[Samatey/2#Comparison_with_Thermotoga]] which has buttons that animate the alignments of different domains.
Line 318: Line 308:
===PyMOL===
===PyMOL===
*Download site: [http://www.pymol.org/ PyMOL.Org]
*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].
*Color by RMSD: YES [http://www.pymolwiki.org/index.php/ColorByRMSD example].


===UCSF Chimera===
===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]
*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===
===TopMatch===
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===Example Requiring Flexibility===
===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:
*CE:
**4.8 &Aring; RMSD.
**4.8 &Aring; RMSD.
Line 355: Line 344:
Example 1<br>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, &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>
</td></tr><tr><td>
CE</td><td>305</td><td>3.2</td><td>96/401
CE</td><td>305</td><td>3.2</td><td>96/401
Line 377: Line 366:
Example 2<br>Mammalian tubulin &alpha; vs. &beta;, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.
Example 2<br>Mammalian tubulin &alpha; vs. &beta;, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.
</td></tr><tr><td>
</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>
</td></tr><tr><td>
CE</td><td>404</td><td>1.34</td><td>56/"460"(?)
CE</td><td>404</td><td>1.34</td><td>56/"460"(?)
Line 390: Line 379:
<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 &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.
*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====
====Dali example====
*3.2 &Aring; RMSD RIGID alignment included 299 residues.
*3.2 &Aring; RMSD RIGID superposition included 299 residues.
*Z-score: 25.5.
*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.
*The structure-based sequence alignment has many gaps.


Line 406: Line 395:
Tested with version 4.01 OS X.
Tested with version 4.01 OS X.
*Magic Fit -- SEQUENCED-BASED:
*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:
*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.
**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 &Aring; for 64 aligned residues.
**1.0 &Aring; for 64 superposed residues.


====FATCAT example====
====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).
*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.
*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====
====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.
*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 &Aring; RMSD for 197 aligned residues.
**4.5 &Aring; RMSD for 197 superposed residues.


====TM-Align example====
====TM-Align example====
*3.42 &Aring; for 312 aligned residues.
*3.42 &Aring; for 312 superposed residues.
*Structure-based sequence alignment is displayed.
*Structure-based sequence alignment is displayed.


====TopMatch example====
====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====
====VAST example====
* 4.0 &Aring; RMSD for 299 aligned residues.
* 4.0 &Aring; RMSD for 299 superposed residues.
* Expectation value: 10<sup>-16</sup>.
* 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.'''
* '''I could find no way to download the aligned PDB file for visualization in Jmol or RasMol.'''


==References==
==References==
<references />
<references />

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
Retrieved from "https://proteopedia.openfox.io/w/Structure_superposition_tools"