User:Eric Martz/Sandbox 11

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Contents

Structural Alignment Tools

Structural Alignment Servers

Alphabetical, by server name:

CE

The Combinatorial Extension structural alignment server.

  • Server: CE.
  • Publication (1998)[1]
  • N.B. Database of structure neighbors has not been updated since 2001. Java applet for viewing results is not working in Sept. 2010.
  • Rigid alignment: ONLY (according to FATCAT[2])
  • Structure-based sequence alignment: YES.

DALI

  • Rigid alignment: ONLY (according to FATCAT[2])

FATCAT

  • Server: fatcat.burnham.org Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT)
  • Publication (2003)[2] "... 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"[3] 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[4], FATCAT obtained similar RMSD's and aligned lengths with fewer twists (hinges).

FlexProt

  • Server: FlexProt.
  • Publication (2002)[5]
  • 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.

VAST

Rigid alignment: ONLY (according to FATCAT[2])

Structural Alignment Software

Example

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:
    • RMSD=4.8 Å.
    • 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.

References

  1. ↑ Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1998 Sep;11(9):739-47. PMID:9796821
  2. ↑ 2.0 2.1 2.2 2.3 Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003 Oct;19 Suppl 2:ii246-55. PMID:14534198
  3. ↑ 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.
  4. ↑ Shatsky M, Nussinov R, Wolfson HJ. Flexible protein alignment and hinge detection. Proteins. 2002 Aug 1;48(2):242-56. PMID:12112693 doi:10.1002/prot.10100
  5. ↑ Shatsky M, Nussinov R, Wolfson HJ. Flexible protein alignment and hinge detection. Proteins. 2002 Aug 1;48(2):242-56. PMID:12112693 doi:10.1002/prot.10100

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Eric Martz

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