Structure superposition tools

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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[1].

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:

  1. Pairwise superposition. All servers listed below enable you to upload two 3D models (or specify them from the PDB) and generate a structure superposition.
  2. Structure neighbors. Some servers (notably Dali, FATCAT, VAST and 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 list of structure superposition software packages and an overview of structure superposition. Hasegawa and Holm reviewed structure superposition methods in 2009[2].

Contents

Evaluating Structure Superpositions

The structural differences between two optimally superposed models are usually measured as the 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[3]. Crystallographic models of proteins with about 50% sequence identity differ by about 1 Å RMSD[3][4]. Deviations can be much larger for models determined by NMR[4].

The statistical significance of a structure superposition, relative to a superposition of random sequence-nonredundant structures in the PDB, is usually measured with a 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 GDT_TS. See also Theoretical models.

Visualizing Structure Superpositions

Structural alignment of 1fsz with 1tub.

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 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 except that the target color has been changed to make it more distinct from the red query. (.)
  • 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 superposition is 3.2 Å.)

  • This was generated by 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 and 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. 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 rigid superposition only.
  • Dali rigid superposition only. Jmol. Colors by structure conservation distinguishing closely superposed from poorly superposed segments.
  • FATCAT flexible and rigid superposition. Jmol. Generates morph of alignment.
  • TopMatch

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

DNA structure superposition

None of the above servers does structure superposition of DNA, but 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 can superpose multiple chains, including both protein and DNA chains in a single superposition (Iterative Magic Fit). TopMatch and TopSearch can also superpose multichain protein assemblies.

One chain vs. many other chains

Dali, FATCAT, VAST and 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 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 explanation of CE methodology at Wikipedia.

  • Server: Use rcsb.org At the main page, click on Analyze, then on Pairwise Structure Alignment.
  • Publication (1998)[5]
  • Rigid alignment: ONLY (according to FATCAT[6])
  • 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 explanation of Dali's methods at Wikipedia.

  • Server: Dali Server
  • Publication 2010[7], 2020[8].
  • 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[6])
  • 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: fatcat.godziklab.org Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT)
  • Publication (2003)[6] "... 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"[9] 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[10], FATCAT obtained similar RMSD's and aligned lengths with fewer twists (hinges).

FlexProt

  • Server: FlexProt.
  • Publication (2002)[11]
  • 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 provides evidence that it out-performs FlexProt.

MAMMOTH

  • Server: mammoth MAMMOTH (MAtching Molecular Models Obtained from THeory)
  • Publication (2002)[12]
  • 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: RUPEE
  • Publication (2019)[13]
  • 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: SuperPose
  • Publication (2004)[14]
  • 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: TM-align
  • Publication (2005)[12]
  • 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: TopMatch
  • Publications (both 2008)[15][16], (2012)[17]
  • 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).
  • Pairwise superposition including uploaded models: YES
  • Visualization: YES.
  • Color by deviation: NO.
  • Offered by RCSB? NO.
  • Special features:
    • Structure superposition of multiprotein complexes.
    • 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: TopSearch
  • Publication (2014)[18]
  • 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).
  • Search with uploaded models: YES
  • Visualization: YES.
  • Color by deviation: NO.
  • Special features: Structure search of multichain protein complexes.

VAST

  • Server: Vector Alignment Search Tool
  • Publications 1996[15], 2014[19], 2020[20].
  • Help on server: YES.
  • Does superposition involve sequence comparison? UNCLEAR.
  • Rigid superposition: ONLY (according to FATCAT[6])
  • 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: Structure Navigator but server not found in 2021.
  • Publication (2007): 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: DeepView Swiss-PdbViewer.
  • Publications (1997, 1999)[21][22]
  • 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

PyMOL

  • Download site: PyMOL.Org
  • The super command does structural superposition.
  • Color by RMSD: YES example.

UCSF Chimera

TopMatch

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

Example 1
Summary for 1fszA vs. 1tubA

ToolResidues SuperposedRMSD, ÅResidues Not Superposed/Total
CE3053.296/401
Dali2993.2Not Reported
DeepView159
64
1.69
1.0
FATCAT2983.02103/401
MAMMOTH298?4.0?
PyMOL1974.5
TM-align3123.4
TopMatch2752.9
VAST2994.0

Example 2
Mammalian tubulin α vs. β, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.

ToolResidues SuperposedRMSD, ÅResidues Not Superposed
CE4041.3456/"460"(?)
Dali4201.620/?
DeepView3891.1122/437
FATCAT4241.7516
PyMOL3250.90
Topmatch4161.68

1fsz is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin[23][24] 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

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