Structure superposition tools

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. This may suggest evolutionary relationships that are not discernable from sequence comparisions. Hasegawa and Holm reviewed structural alignment methods in 2009.

The structural differences between two optimally aligned models are usually measured as the Root Mean Square Distance (RMSD) between the aligned alpha-carbon positions (excluding deviations from the non-aligned positions). The statistical significance of a structural alignment, relative to an alignment 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 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.

Wikipedia offers a list of structural alignment software packages and an overview of structural alignment.

Structural Alignment ServersStructural Alignment Servers

Alphabetical, by server name:

CECE

The Combinatorial Extension structural alignment server.

• Server: CE Home Page.
• Publication (1998)
• 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)
• 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).

DaliDali

"Dali does not optimize RMSD, it matches contacts" (Dali Tutorial, section 4.4.2).

• Server: Dali Server
• Publication (2010)
• 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)
• Flexible alignment: NO.
• Structure neighbors (pre-calculated): YES
• 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).

FATCATFATCAT

• Server: fatcat.burnham.org Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT)
• Publication (2003) "... 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
• 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 ..."). Produces a sequence alignment. Offers a RasMol script to color each rigid segment distinctly (separated by twists/hinges).

Notes from the publication: With 10 "difficult examples" 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, FATCAT obtained similar RMSD's and aligned lengths with fewer twists (hinges).

FlexProtFlexProt

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

MAMMOTHMAMMOTH

• Server: mammoth MAMMOTH (MAtching Molecular Models Obtained from THeory)
• Publication (2002)
• 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

TM-AlignTM-Align

• Server: TM-align
• Publication (2005)
• 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

TopMatchTopMatch

• Server: TopMatch
• Publications (both 2008)
• Help on server: YES.
• Does alignment involve sequence comparison? UNCLEAR.
• Rigid alignment: YES.
• Flexible alignment: NO.
• Multiple alignment: NO.
• Structure neighbors (pre-calculated): NO.
• Pairwise alignment including uploaded models: YES
• Visualization: Jmol.
• Color by deviation: NO.
• Offered by RCSB? YES
• Special features: You can download the aligned target PDB file (in a separate file from the query PDB file). A PyMOL script is also available.

VASTVAST

• Server: Vector Alignment Search Tool
• Publication (1996)
• Help on server: YES.
• Does alignment involve sequence comparison? UNCLEAR.
• Rigid alignment: ONLY (according to 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.

Structural Alignment SoftwareStructural Alignment Software

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

Calculate Structure AlignmentCalculate Structure Alignment

This is a java program (java web start) offered by the U.S. PDB. At 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. Eric Martz 16:28, 4 October 2010 (IST)
• Help is minimal and results are not clearly labeled.

DeepView = Swiss-PDBViewerDeepView = Swiss-PDBViewer

• Download site: DeepView Swiss-PdbViewer.
• Publications (1997, 1999)
• 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, Explore Domain Alternate Fits: does a sequence-independent structural alignment.
• 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.

ExamplesExamples

Example Requiring FlexibilityExample 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.

Example for Rigid AlignmentExample for Rigid Alignment

1fsz is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin found in 1tub chain A, length 440. However, the sequence identity is very low (~12%).

CE exampleCE 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.
• Same results obtained at either the CE website, or using the Calculate Structure Alignment java webstart software (see above).

Dali exampleDali example

• 3.2 Å RMSD RIGID alignment included 299 residues.
• Z-score: 25.5.
• The structure-based sequence alignment has many gaps.

DeepView = Swiss-PDBViewer exampleDeepView = 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 exampleFATCAT 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).
• FLEXIBLE alignment introduced ZERO twists (hinges), so gave the same result as the rigid alignment.
• The structure-based sequence alignment has many gaps, looking similar to that generated by CE.

MAMMOTH exampleMAMMOTH example

• 4.0 Å (?) with 298 aligned residues (?) (Labeling in results is unclear.)
• Structure-based sequence alignment is displayed.

TM-Align exampleTM-Align example

• 3.42 Å for 312 aligned residues.
• Structure-based sequence alignment is displayed.

TopMatch exampleTopMatch example

• Error # 1063, no explanation. No structures displayed in Jmol.
• 3.1 Å RMSD. Alignment includes 251 residues. Sequence identity in the aligned regions is 12%.
• Structure-based sequence alignment is displayed.
• Tried the example requiring flexibility (above) as a second case. A 40 residue subdomain was aligned with RMSD 1.8 Å, and the alignment was displayed in Jmol with no error.

VAST exampleVAST 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.