Proteopedia - User contributions [en]

Structure superposition tools

2023-09-11T08:36:07Z

Markus Wiederstein: added publication on TopMatch-web (2020)

''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 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 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 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 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 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 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 Å 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 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, 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 Structure Superpositions==
<applet size='400' frame='true' align='right' caption='Structural alignment of [[1fsz]] with [[1tub]].'
scene='Structural_alignment_tools/Dali_chains_ab_water/1' />
Structure superpositions are usually visualized as the superposed backbone traces of the models. The example at right shows the bacterial cell division protein FtsZ ([[1fsz]]:A) superposed by [[#Dali|Dali]] with mammalian tubulin ([[1tub]]:A). Sequence identity in the superposed regions is about 13%.
*The non-superposed segments are white in the query (FtsZ) and thin in the target (tubulin). 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 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 (FtsZ) and backbone for target (tubulin) where the target α carbons are within 3.5 Å. (The RMSD for this [[#Dali|Dali]] superposition is 3.2 Å.)
<jmol>
<jmolButton>
<script>
startRes = 1;
select all
set labelpointer on
function dispSeg()
{
endRes = startRes + 49
dispRange = ("" + startRes + "-" + endRes)
display (:a.ca and @dispRange)
display displayed or (:b.ca and within(3.5, displayed))
startSel = "" + startRes + ":a.ca"
endSel = "" + endRes + ":a.ca"
select @startSel
label @startRes
select @endSel
label @endRes
}
dispSeg();
</script>
<text>Show 1-50</text>
</jmolButton>
<jmolButton>
<script>
startRes += 50;
dispSeg();
</script>
<text>Next 50</text>
</jmolButton>
</jmol>
* 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 Å 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 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==
===Protein structural superposition===
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 superposition only.
* [[#Dali|Dali]] rigid superposition only. Jmol. Colors by ''structure conservation'' distinguishing closely superposed from poorly superposed segments.
* [[#FATCAT|FATCAT]] '''flexible''' and rigid superposition. Jmol. Generates '''morph''' of alignment.
* [[#TopMatch|TopMatch]]

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

===Multiple chain structure superposition===
====Multiple chains in each of two models====
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====
[[#Dali|Dali]], [[#FATCAT|FATCAT]], [[#VAST|VAST]] and [[#TopSearch|TopSearch]] enable you to upload a 3D model, or specify a [[PDB code]], and obtain a list of the most similar structures in the [[PDB]], called '''structure neighbors'''.

====One protein complex vs. many other protein complexes====
In addition to a search on the level of single chains, [[#TopSearch|TopSearch]] provides you with a list of the most similar protein complexes (biological assemblies) given a (possibly uploaded) protein complex.

==Structural Alignment Servers==
Alphabetical, by server name:

===CE===
The ''Combinatorial Extension'' method. See the [http://en.wikipedia.org/wiki/Structural_alignment#Combinatorial_extension explanation of CE methodology at Wikipedia].
*Server: Use [http://rcsb.org rcsb.org] At the main page, click on Analyze, then on Pairwise Structure Alignment.
*Publication (1998)<ref>PMID: 9796821</ref>

*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
*Align DNA? NO.
*Align multiple protein chains? NO. Aligns one pair of chains at a time.
*Structure-based sequence alignment: YES.
*Visualization: Mol*.
*Offered by RCSB? YES.

===Dali===
"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]
*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.
*Does the structure superposition involve sequence comparison? UNCLEAR.
*Rigid superposition: YES (section 4.4.2 of the Dali Tutorial). ONLY (according to FATCAT<ref name="fatcat" />)
*Flexible superposition: NO.
*Structure neighbors (pre-calculated): YES
*Superpose DNA? NO.
*Superpose multiple protein chains? YES? (Results are inadequately labeled and confusing.)
*Pairwise superposition including uploaded models: YES
*Ligands: KEPT.
*Visualization: YES. No color key on the visualization page.
*Color by deviation: YES ("Structure Conservation").
*Offered by RCSB? NO.
*Special features:
**Colors 3D visualization by sequence conservation, calculated from the checked models. No color key on the visualization page.

===FATCAT===

*Server: [http://fatcat.godziklab.org/ fatcat.godziklab.org] Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT)
*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.
*Does superposition involve sequence comparison? UNCLEAR.
*Rigid superposition: YES (optional)
*Flexible superposition: YES (optional)
*Structure neighbors (pre-calculated): YES
*Pairwise superposition including uploaded models: YES
*Superpose DNA: NO.
*Superpose multiple protein chains: NO. Aligns a single pair of chains at a time.
*Structure-based sequence alignment: YES
*Visualization: YES.
*Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)
*Offered by RCSB? YES
*Special features:
**Produces a [[morph]] between the two superposed chains (at the link "Interpolating between ...").
**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 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===

*Server: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt].
*Publication (2002)<ref>PMID: 12112693</ref>
*Rigid superposition: YES (Results include alignment for 0 hinges, but only a well-aligning subset of residues are aligned.)
*Flexible superposition: YES (Results are given for various numbers of hinges.)
*Visualization: '''NONE''' (You can download PDB files.)
*Ligands: '''Discarded'''.
*Special features: Assigns a distinct chain name to each rigid segment separated by a hinge, facilitating informative coloring.
Note: [[#FATCAT|FATCAT]] provides evidence that it out-performs FlexProt.

===MAMMOTH===
*Server: [http://ub.cbm.uam.es/servers/mammoth/mammoth.php mammoth MAMMOTH] (MAtching Molecular Models Obtained from THeory)
*Publication (2002)<ref name="mammoth">PMID: 12381844</ref>
*Help on server: Little or none.
*Does superposition involve sequence comparison? NO: They state that this is a "sequence-independent structural alignment".
*Rigid superposition: YES.
*Flexible superposition: NO.
*Multiple superposition: YES.
*Structure neighbors (pre-calculated): NO.
*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.''')
*Color by deviation: '''NO'''.
*Offered by RCSB? NO.

===RUPEE===

*Server: [https://ayoubresearch.com RUPEE]
*Publication (2019)<ref name="rupee">PMID: 30875409</ref>
*Help on server: YES.
*Structure neighbors (pre-calculated): NO.
*Does superposition involve sequence comparison? NO.
*Rigid superposition: YES.
*Flexible superposition: NO.
*Multiple superposition: NO.
*Structure-based sequence alignment: YES
*Search with uploaded models: YES
*Visualization: YES.
*Color by deviation: NO.
*Special features:
**Purely geometric structure search with no dependence on sequence.
**For each result, provides a 3d structure superposition, a sequence alignment, and a downloadable PDB superposition file.
**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===

*Server: [http://wishart.biology.ualberta.ca/SuperPose/ SuperPose]
*Publication (2004)<ref name="superpose">PMID: 15215457 </ref>
*Help on server: ?
*Structure neighbors (pre-calculated): ?
*Visualization: ?
*Does superposition involve sequence comparison: ?
*Rigid superposition: ?
*Flexible superposition: ?
*Multiple superposition: YES.
*Structure-based sequence alignment: ?
*Search with uploaded models: YES
*Color by deviation: ?
*Special features: ?

===TM-Align===

*Server: [http://zhanglab.ccmb.med.umich.edu/TM-align/ TM-align]
*Publication (2005)<ref name="mammoth">PMID: 15849316</ref>
*Help on server: A little.
*Does superposition involve sequence comparison? UNCLEAR.
*Rigid superposition: YES.
*Flexible superposition: NO.
*Multiple superposition: You can download the software to run on linux.
*Structure neighbors (pre-calculated): NO.
*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.)
*Color by deviation: '''NO'''.
*Offered by RCSB? YES.

===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>, (2020)<ref name="topmatch4">PMID: 32479639</ref>
*Help on server: YES.
*Does superposition involve sequence comparison? NO.
*Rigid superposition: YES.
*Flexible superposition: NO.
*Multiple superposition: NO.
*Structure-based sequence alignment: YES.
*Structure neighbors (pre-calculated): NO (but see [[#TopSearch|TopSearch]]).
*Pairwise superposition including uploaded models: YES
*Visualization: YES.
*Color by deviation: NO.
*Offered by RCSB? NO.
*Special features:
**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.

===TopSearch===

*Server: [http://topsearch.services.came.sbg.ac.at/ TopSearch]
*Publication (2014)<ref name="topsearch">PMID: 24954616</ref>
*Help on server: YES.
*Structure neighbors (pre-calculated): YES.
*Does superposition involve sequence comparison? NO.
*Rigid superposition: YES.
*Flexible superposition: NO.
*Multiple superposition: NO.
*Structure-based sequence alignment: YES (indirectly, via link to [[#TopMatch|TopMatch]]).
*Search with uploaded models: YES
*Visualization: YES.
*Color by deviation: NO.
*Special features: Structure search of multichain protein complexes.

===VAST===
*Server: [http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml Vector Alignment Search Tool]
*Publications 1996<ref name="topmatch">PMID: 8804824</ref>, 2014<ref>PMID: 24319143</ref>, 2020<ref>PMID: 32006286</ref>.
*Help on server: YES.
*Does superposition involve sequence comparison? UNCLEAR.
*Rigid superposition: ONLY (according to FATCAT<ref name="fatcat" />)
*Flexible superposition: NO.
*Multiple superposition: ?.
*Structure neighbors (pre-calculated): YES.
*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).
*Offered by RCSB? NO.
*Special features:

Note: In order to get alignment parameters such as RMSD, you must change the list format from ''graphics'' to ''table'', then click the List button.

===Structure Navigator of PDB-Japan===
*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 superposition involve sequence comparison? Yes, and the sequence alignment for each pair is displayed.
*Rigid superposition: YES.
*Flexible superposition: (Probably not -- unclear.)
*Multiple superposition: ??
*Structure neighbors (pre-calculated): ??
*Pairwise alignment including uploaded models: YES.
*Visualization: Yes, using the jV applet developed at PDBj.
*Color by deviation: No?
*Offered by RCSB? NO.
*Special features: ??

==Structural Superposition Software==
This section is for stand-alone software packages that do not require a web browser.

===DeepView = Swiss-PDBViewer===
*Download site: [http://www.expasy.org/spdbv/ DeepView Swiss-PdbViewer].
*Publications (1997, 1999)<ref>PMID: 9504803</ref><ref>PMID: 10470037</ref>
*Version 4.11 released in 2019; works on Windows and macOS 10.5-10.14.
*'''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 superposition.
* 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 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.
* Fit, Set Layer Std Dev. into B-factors: works only when the sequences of the aligned models are identical.

===Jmol===
See
* [[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.
* [[Samatey/3#Comparison_with_Salmonella]]: the button ''Animate Structural Alignment'' plays a long "movie script", but in August 2018 that appears to hang in the middle. This problem may have arisen when Proteopedia was converted to use JSmol.

===PyMOL===
*Download site: [http://www.pymol.org/ PyMOL.Org]
*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 www.cgl.ucsf.edu/chimera/download.html]
*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===
*Download site: [https://www.came.sbg.ac.at/app_download.php?app=topmatch TopMatch stand-alone]
*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>, (2012)<ref name="topmatch3">PMID: 22483118</ref>
*Available for Linux and Windows.
*Features: see [[#TopMatch|TopMatch-web]]

==Examples==

===Example Requiring Flexibility===

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 Å RMSD.
**38.5% sequence identity in structure-based sequence alignment. Aligned/gap positions = 109/47.
**Uses old, unremediated PDB files (1cfc has no chain A).
*FATCAT:
**5 hinges(twists): 140 residues aligned, RMSD 2.08 Å.
*FlexProt:
**0 hinges: 49 residues aligned, RMSD 2.94 Å.
**1 hinge: 84 residues aligned, RMSD 2.97 Å.
**2 hinges: 102 residues aligned, RMSD 2.82 Å.
**3 hinges: 118 residues aligned, RMSD 2.60 Å.
**4 hinges: 134 residues aligned, RMSD 2.62 Å.

===Examples for Rigid Alignment===
<table align="right" border="1" cellpadding="4" hspace="6" width="350"><tr><td colspan="4" bgcolor="#d0d0d0">
Example 1 Summary for 1fszA vs. 1tubA
</td></tr><tr><td>
Tool</td><td>Residues Superposed</td><td>RMSD, Å</td><td>Residues Not Superposed/Total
</td></tr><tr><td>
CE</td><td>305</td><td>3.2</td><td>96/401
</td></tr><tr><td>
Dali</td><td>299</td><td>3.2</td><td>Not Reported
</td></tr><tr><td>
DeepView</td><td>159 64</td><td>1.69 1.0</td><td>
</td></tr><tr><td>
FATCAT</td><td>298</td><td>3.02</td><td>103/401
</td></tr><tr><td>
MAMMOTH</td><td>298?</td><td>4.0?</td><td>
</td></tr><tr><td>
PyMOL</td><td>197</td><td>4.5</td><td>
</td></tr><tr><td>
TM-align</td><td>312</td><td>3.4</td><td>
</td></tr><tr><td>
TopMatch</td><td>275</td><td>2.9</td><td>
</td></tr><tr><td>
VAST</td><td>299</td><td>4.0</td><td>
</td></tr><tr><td colspan="4" bgcolor="#d0d0d0">
Example 2 Mammalian tubulin α vs. β, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.
</td></tr><tr><td>
Tool</td><td>Residues Superposed</td><td>RMSD, Å</td><td>Residues Not Superposed
</td></tr><tr><td>
CE</td><td>404</td><td>1.34</td><td>56/"460"(?)
</td></tr><tr><td>
Dali</td><td>420</td><td>1.6</td><td>20/?
</td></tr><tr><td>
DeepView</td><td>389</td><td>1.11</td><td>22/437
</td></tr><tr><td>
FATCAT</td><td>424</td><td>1.75</td><td>16
</td></tr><tr><td>
PyMOL</td><td>325</td><td>0.90</td><td>
<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). '''Tests in this section were performed in 2011.'''
====CE example====
*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.
*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.

====Dali example====
*3.2 Å RMSD RIGID superposition included 299 residues.
*Z-score: 25.5.
*13% sequence identity for the structurally superposed regions.
*The structure-based sequence alignment has many gaps.

====DeepView = Swiss-PDBViewer example====
Tested with version 4.01 OS X.
*Magic Fit -- SEQUENCED-BASED:
**4.4 Å RMSD for 114 superposed residues.
*Iterative Magic Fit -- Sequence based followed by RMSD minimization:
**1.69 Å RMSD for 159 superposed residues.
*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 Å for 64 superposed residues.

====FATCAT example====
*3.02 Å RMSD RIGID superposition includes 298 residues.
*P value: 5 x 10-8 (used instead of z-score to take twists into account).
*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 superposition introduced ZERO twists (hinges), so gave the same result as the rigid superposition.

====MAMMOTH example====
*4.0 Å (?) 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 Å RMSD for 197 superposed residues.

====TM-Align example====
*3.42 Å for 312 superposed residues.
*Structure-based sequence alignment is displayed.

====TopMatch example====
*2.9 Å RMSD. Superposition includes 275 residues.
*13% sequence identity in the superposed regions.
*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====
* 4.0 Å RMSD for 299 superposed residues.
* Expectation value: 10-16.
* 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 />

User:Markus Wiederstein/Sandbox 1

2016-12-02T09:27:05Z

Markus Wiederstein:

==Crystal Structure of Human Acetylcholinesterase==
<StructureSection load='4pqe' size='340' side='right' caption='[[4pqe]], [[Resolution|resolution]] 2.90Å' scene=''>
__TOC__
== Structural highlights ==
<table><tr><td colspan='2'>[[4pqe]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PQE OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PQE FirstGlance]. 
</td></tr><tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[3lii|3lii]], [[4ey4|4ey4]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Acetylcholinesterase Acetylcholinesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.7 3.1.1.7] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pqe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pqe RCSB], [http://www.ebi.ac.uk/pdbsum/4pqe PDBsum], [https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe&pdbitem=asu TopSearch]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/ACES_HUMAN ACES_HUMAN]] Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis.<ref>PMID:2714437</ref> <ref>PMID:1748670</ref> <ref>PMID:1517212</ref> <ref>PMID:11985878</ref>
== Structural relationships in TopSearch ==
[https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe@1&pdbitem=biu Biological assemblies]

[https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe,A&pdbitem=chain Chains]

[https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe&pdbitem=asu Asymmetric units]
== References ==
<references/>
</StructureSection>

User:Markus Wiederstein/Sandbox 1

2016-12-02T09:23:28Z

Markus Wiederstein:

==Crystal Structure of Human Acetylcholinesterase==
<StructureSection load='4pqe' size='340' side='right' caption='[[4pqe]], [[Resolution|resolution]] 2.90Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4pqe]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PQE OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PQE FirstGlance]. 
</td></tr><tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[3lii|3lii]], [[4ey4|4ey4]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Acetylcholinesterase Acetylcholinesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.7 3.1.1.7] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pqe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pqe RCSB], [http://www.ebi.ac.uk/pdbsum/4pqe PDBsum], [https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe&pdbitem=asu TopSearch]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/ACES_HUMAN ACES_HUMAN]] Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis.<ref>PMID:2714437</ref> <ref>PMID:1748670</ref> <ref>PMID:1517212</ref> <ref>PMID:11985878</ref>
== Structural relationships in TopSearch ==
[https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe@1&pdbitem=biu Biological assemblies]

[https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe,A&pdbitem=chain Chains]

[https://topsearch.services.came.sbg.ac.at/?code=4pqe&query=4pqe&pdbitem=asu Asymmetric units]
== References ==
<references/>
__TOC__
</StructureSection>

User:Markus Wiederstein/Sandbox 1

2016-12-02T09:11:51Z

Markus Wiederstein:

==Crystal Structure of Human Acetylcholinesterase==
<StructureSection load='4pqe' size='340' side='right' caption='[[4pqe]], [[Resolution|resolution]] 2.90Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4pqe]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PQE OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PQE FirstGlance]. 
</td></tr><tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[3lii|3lii]], [[4ey4|4ey4]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Acetylcholinesterase Acetylcholinesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.7 3.1.1.7] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pqe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pqe RCSB], [http://www.ebi.ac.uk/pdbsum/4pqe PDBsum]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/ACES_HUMAN ACES_HUMAN]] Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis.<ref>PMID:2714437</ref> <ref>PMID:1748670</ref> <ref>PMID:1517212</ref> <ref>PMID:11985878</ref>
== Structural relationships in TopSearch ==
[https://topsearch.services.came.sbg.ac.at/?code=1crn&query=1crn&pdbitem=bio Biological assemblies]

[https://topsearch.services.came.sbg.ac.at/?code=1crn&query=1crn&pdbitem=chn Chains]

[https://topsearch.services.came.sbg.ac.at/?code=1crn&query=1crn&pdbitem=asu Asymmetric units]
== References ==
<references/>
__TOC__
</StructureSection>

User:Markus Wiederstein/Sandbox 1

2016-12-01T17:21:19Z

Markus Wiederstein: New page: ==Your Heading Here (maybe something like 'Structure')== 2 <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for y...

==Your Heading Here (maybe something like 'Structure')== 2
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Markus Wiederstein/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

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

User:Markus Wiederstein

2016-12-01T17:20:06Z

Markus Wiederstein: added sandbox link

* Full Real Name: Markus Wiederstein

* Position: Associate Professor

* Institution (NO ABBREVIATIONS): University of Salzburg

* City, State/Province, Country: Salzburg, Austria

* Field of Expertise or Study: protein structure comparison/classification/validation/prediction/design

*[[User:Markus Wiederstein/Sandbox 1]]

Structure superposition tools

2016-10-20T15:52:13Z

Markus Wiederstein: revised sections on TopMatch (additional reference, ...); added section on TopSearch

''Structural alignment'' refers to the alignment, in three dimensions, between two or more molecular models. In the case of proteins, this is usually performed without reference to the sequences of the proteins. When the models align well, 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 alignment. Characteristics of structural alignment servers and software packages are listed, along with results of testing with a few examples.

There are two common applications of structural alignment servers:
# '''Pairwise alignment'''. All servers listed below enable you to upload two 3D models (or specify them from the [[PDB]]) and generate a structural alignment.
# '''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 alignments between your query structure versus each structure in the [[PDB]].

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

==Evaluating Structural Alignments==
The structural differences between two optimally aligned models are usually measured as the [http://en.wikipedia.org/wiki/RMSD Root Mean Square Deviation] ('''RMSD''') between the aligned alpha-carbon positions (excluding deviations from the non-aligned 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 Å 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 alignment, relative to an alignment 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.

==Visualizing Structural Alignments==
<applet size='400' frame='true' align='right' caption='Structural alignment of [[1fsz]] with [[1tub]].'
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 FtsZ ([[1fsz]]:A) aligned by [[#Dali|Dali]] with mammalian tubulin ([[1tub]]:A). Sequence identity in the structurally aligned regions is about 13%.
*The non-aligned segments are white in the query (FtsZ) and thin in the target (tubulin). 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 (FtsZ) and backbone for target (tubulin) where the target α carbons are within 3.5 Å. (The RMSD for this [[#Dali|Dali]] alignment is 3.2 Å.)
<jmol>
<jmolButton>
<script>
startRes = 1;
select all
set labelpointer on
function dispSeg()
{
endRes = startRes + 49
dispRange = ("" + startRes + "-" + endRes)
display (:a.ca and @dispRange)
display displayed or (:b.ca and within(3.5, displayed))
startSel = "" + startRes + ":a.ca"
endSel = "" + endRes + ":a.ca"
select @startSel
label @startRes
select @endSel
label @endRes
}
dispSeg();
</script>
<text>Show 1-50</text>
</jmolButton>
<jmolButton>
<script>
startRes += 50;
dispSeg();
</script>
<text>Next 50</text>
</jmolButton>
</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 Å 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.

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.

==Conclusions==
===Protein structural alignment===
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
* [[#CE|CE]] rigid alignment only (see Note below).
* [[#Dali|Dali]] rigid alignment only. Jmol. Colors by ''structure conservation'' distinguishing aligned from non-aligned segments.
* [[#FATCAT|FATCAT]] '''flexible''' and rigid alignment. Jmol. Generates '''morph''' of alignment.
* [[#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]]).

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

===Multiple chain structural alignment===
====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.

====One chain vs. many other chains====
[[#Dali|Dali]], [[#FATCAT|FATCAT]], [[#VAST|VAST]] and [[#TopSearch|TopSearch]] enable you to upload a 3D model, or specify a [[PDB code]], and obtain a list of the most similar structures in the [[PDB]], called '''structure neighbors'''.

====One protein complex vs. many other protein complexes====
In addition to a search on the level of single chains, [[#TopSearch|TopSearch]] provides you with a list of the most similar protein complexes (biological assemblies) given a (possibly uploaded) protein complex.

==Structural Alignment Servers==
Alphabetical, by server name:

===CE===
The ''Combinatorial Extension'' structural alignment server. 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].
*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.'''
*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
*Align DNA? NO.
*Align multiple protein chains? NO. Aligns one pair of chains at a time.
*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).
*Offered by RCSB? YES.

===Dali===
"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_server/start Dali Server]
*Publication (2010)<ref name="dali">PMID: 20457744</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.
*Does the structural alignment involve sequence comparison? UNCLEAR.
*Rigid alignment: YES (section 4.4.2 of the Dali Tutorial). ONLY (according to FATCAT<ref name="fatcat" />)
*Flexible alignment: NO.
*Structure neighbors (pre-calculated): YES
*Align DNA? NO.
*Align multiple protein chains? YES? (Results are inadequately labeled and confusing.)
*Pairwise alignment including uploaded models: YES
*Ligands: KEPT.
*Visualization: Jmol.
*Color by deviation: '''NO'''.
*Offered by RCSB? NO.
*Special features:
**Colors 3D visualization in Jmol by sequence conservation, calculated from the checked models.
**Colors 3D visualization in Jmol by structure conservation (red for aligned portions, white for unaligned portions).

===FATCAT===

*Server: [http://fatcat.burnham.org/ fatcat.burnham.org] Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT)
*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.
*Does alignment involve sequence comparison? UNCLEAR.
*Rigid alignment: YES (optional)
*Flexible alignment: YES (optional)
*Structure neighbors (pre-calculated): YES
*Pairwise alignment including uploaded models: YES
*Align DNA: NO.
*Align multiple protein chains: NO. Aligns a single pair of chains at a time.
*Structure-based sequence alignment: YES
*Visualization: Jmol or Chime. See ''Special features''.
*Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)
*Offered by RCSB? YES
*Special features:
**Produces a morph between the two aligned chains (at the link "Interpolating between ...").
**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).

===FlexProt===

*Server: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ FlexProt].
*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.)
*Flexible alignment: YES (Results are given for various numbers of hinges.)
*Visualization: '''NONE''' (You can download PDB files.)
*Ligands: '''Discarded'''.
*Special features: Assigns a distinct chain name to each rigid segment separated by a hinge, facilitating informative coloring.
Note: [[#FATCAT|FATCAT]] provides evidence that it out-performs FlexProt.

===MAMMOTH===
*Server: [http://ub.cbm.uam.es/servers/mammoth/mammoth.php mammoth MAMMOTH] (MAtching Molecular Models Obtained from THeory)
*Publication (2002)<ref name="mammoth">PMID: 12381844</ref>
*Help on server: Little or none.
*Does alignment involve sequence comparison? NO: They state that this is a "sequence-independent structural alignment".
*Rigid alignment: YES.
*Flexible alignment: NO.
*Multiple alignment: YES.
*Structure neighbors (pre-calculated): NO.
*Pairwise alignment 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.''')
*Color by deviation: '''NO'''.
*Offered by RCSB? YES

===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)

===TM-Align===

*Server: [http://zhanglab.ccmb.med.umich.edu/TM-align/ TM-align]
*Publication (2005)<ref name="mammoth">PMID: 15849316</ref>
*Help on server: A little.
*Does alignment involve sequence comparison? UNCLEAR.
*Rigid alignment: YES.
*Flexible alignment: NO.
*Multiple alignment: You can download the software to run on linux.
*Structure neighbors (pre-calculated): NO.
*Pairwise alignment including uploaded models: YES
*Visualization: None (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.''')
*Color by deviation: '''NO'''.
*Offered by RCSB? YES

===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>
*Help on server: YES.
*Does alignment involve sequence comparison? NO.
*Rigid alignment: YES.
*Flexible alignment: NO.
*Multiple alignment: NO.
*Structure-based sequence alignment: YES.
*Structure neighbors (pre-calculated): NO (but see TopSearch).
*Pairwise alignment including uploaded models: YES
*Visualization: JSmol.
*Color by deviation: NO.
*Offered by RCSB? YES
*Special features:
**Structure alignment of multiprotein complexes.
**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.

===TopSearch===

*Server: [http://topsearch.services.came.sbg.ac.at/ TopSearch]
*Publication (2014)<ref name="topsearch">PMID: 24954616</ref>
*Help on server: YES.
*Structure neighbors (pre-calculated): YES.
*Visualization: JSmol.
*Does alignment involve sequence comparison? NO.
*Rigid alignment: YES.
*Flexible alignment: NO.
*Multiple alignment: NO.
*Structure-based sequence alignment: YES (indirectly, via link to [[#TopMatch|TopMatch]]).
*Search with uploaded models: YES
*Visualization: JSmol.
*Color by deviation: NO.
*Special features: Structure search of multichain protein complexes.

===VAST===
*Server: [http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml Vector Alignment Search Tool]
*Publication (1996)<ref name="topmatch">PMID: 8804824</ref>
*Help on server: YES.
*Does alignment involve sequence comparison? UNCLEAR.
*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />)
*Flexible alignment: NO.
*Multiple alignment: NO.
*Structure neighbors (pre-calculated): YES.
*Pairwise alignment 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).
*Offered by RCSB? NO.
*Special features:

Note: In order to get alignment parameters such as RMSD, you must change the list format from ''graphics'' to ''table'', then click the List button.

===Structure Navigator of PDB-Japan===
*Server: [http://www.pdbj.org/doc/help?Structure%20Navigator Structure Navigator]
*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.
*Rigid alignment: YES.
*Flexible alignment: (Probably not -- unclear.)
*Multiple alignment: ??
*Structure neighbors (pre-calculated): ??
*Pairwise alignment including uploaded models: YES.
*Visualization: Yes, using the jV applet developed at PDBj.
*Color by deviation: No?
*Offered by RCSB? NO.
*Special features: ??

==Structural Alignment 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 [http://www.pdb.org the PDB website], look for the box of '''Tools''' on the left hand side, and click on ''Compare Structures''. 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].
*Publications (1997, 1999)<ref>PMID: 9504803</ref><ref>PMID: 10470037</ref>
*Version 4.01 released in 2008.
*'''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.
*Help: YES.
* Fit, Magic Fit does a '''sequence-based''' structural alignment.
* Fit, Iterative Magic Fit starts with a sequence-based structural alignment, then does further structural alignment, minimizing the RMSD.
* Fit, Explore Domain Alternate Fits: does a '''sequence-independent''' structural alignment.
* 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.
* Fit, Set Layer Std Dev. into B-factors: works only when the sequences of the aligned models are identical.

===PyMOL===
*Download site: [http://www.pymol.org/ PyMOL.Org]
*The ''super'' command does structural alignment.
*Color by RMSD: YES [http://www.pymolwiki.org/index.php/ColorByRMSD example].

===TopMatch===
*Download site: [https://www.came.sbg.ac.at/app_download.php?app=topmatch TopMatch stand-alone]
*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>, (2012)<ref name="topmatch3">PMID: 22483118</ref>
*Available for Linux and Windows.
*Features: see [[#TopMatch|TopMatch-web]]

==Examples==

===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.
*CE:
**4.8 Å RMSD.
**38.5% sequence identity in structure-based sequence alignment. Aligned/gap positions = 109/47.
**Uses old, unremediated PDB files (1cfc has no chain A).
*FATCAT:
**5 hinges(twists): 140 residues aligned, RMSD 2.08 Å.
*FlexProt:
**0 hinges: 49 residues aligned, RMSD 2.94 Å.
**1 hinge: 84 residues aligned, RMSD 2.97 Å.
**2 hinges: 102 residues aligned, RMSD 2.82 Å.
**3 hinges: 118 residues aligned, RMSD 2.60 Å.
**4 hinges: 134 residues aligned, RMSD 2.62 Å.

===Examples for Rigid Alignment===
<table align="right" border="1" cellpadding="4" hspace="6" width="350"><tr><td colspan="4" bgcolor="#d0d0d0">
Example 1 Summary for 1fszA vs. 1tubA
</td></tr><tr><td>
Tool</td><td>Residues Aligned</td><td>RMSD, Å</td><td>Unaligned Residues /Total
</td></tr><tr><td>
CE</td><td>305</td><td>3.2</td><td>96/401
</td></tr><tr><td>
Dali</td><td>299</td><td>3.2</td><td>Not Reported
</td></tr><tr><td>
DeepView</td><td>159 64</td><td>1.69 1.0</td><td>
</td></tr><tr><td>
FATCAT</td><td>298</td><td>3.02</td><td>103/401
</td></tr><tr><td>
MAMMOTH</td><td>298?</td><td>4.0?</td><td>
</td></tr><tr><td>
PyMOL</td><td>197</td><td>4.5</td><td>
</td></tr><tr><td>
TM-align</td><td>312</td><td>3.4</td><td>
</td></tr><tr><td>
TopMatch</td><td>275</td><td>2.9</td><td>
</td></tr><tr><td>
VAST</td><td>299</td><td>4.0</td><td>
</td></tr><tr><td colspan="4" bgcolor="#d0d0d0">
Example 2 Mammalian tubulin α vs. β, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.
</td></tr><tr><td>
Tool</td><td>Residues Aligned</td><td>RMSD, Å</td><td>Unaligned Residues
</td></tr><tr><td>
CE</td><td>404</td><td>1.34</td><td>56/"460"(?)
</td></tr><tr><td>
Dali</td><td>420</td><td>1.6</td><td>20/?
</td></tr><tr><td>
DeepView</td><td>389</td><td>1.11</td><td>22/437
</td></tr><tr><td>
FATCAT</td><td>424</td><td>1.75</td><td>16
</td></tr><tr><td>
PyMOL</td><td>325</td><td>0.90</td><td>
<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).
====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.
*Z-score: 6.5.
*12.5% sequence identity within the structural alignment.
*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software (see above).

====Dali example====
*3.2 Å RMSD RIGID alignment included 299 residues.
*Z-score: 25.5.
*13% sequence identity for the structurally aligned regions.
*The structure-based sequence alignment has many gaps.

====DeepView = Swiss-PDBViewer example====
Tested with version 4.01 OS X.
*Magic Fit -- SEQUENCED-BASED:
**4.4 Å RMSD for 114 aligned residues.
*Iterative Magic Fit -- Sequence based followed by RMSD minimization:
**1.69 Å RMSD for 159 aligned residues.
*Explore Domain Alternate Fits -- sequence-independent alignment:
**Used option NOT to use selected residues.
**Nevertheless program complained repeatedly that I had not selected residues.
**Nevertheless program produced an alignment:
**1.0 Å for 64 aligned residues.

====FATCAT example====
*3.02 Å RMSD RIGID alignment includes 298 residues.
*P value: 5 x 10-8 (used instead of z-score to take twists into account).
*10.2% sequence identity in the structurally aligned 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.

====MAMMOTH example====
*4.0 Å (?) with 298 aligned 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 Å RMSD for 197 aligned residues.

====TM-Align example====
*3.42 Å for 312 aligned residues.
*Structure-based sequence alignment is displayed.

====TopMatch example====
*2.9 Å RMSD. Alignment includes 275 residues.
*13% sequence identity in the aligned regions.
*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was aligned with RMSD 2.69 Å, an alternative alignment matching the second domain shows up with 47 residues/RMSD 2.69 Å.

====VAST example====
* 4.0 Å RMSD for 299 aligned residues.
* Expectation value: 10-16.
* 11.4% sequence identity in the aligned segments.
* '''I could find no way to download the aligned PDB file for visualization in Jmol or RasMol.'''

==References==
<references />