RCSB PDB Comparison Tool

Acknowledgements

Smith & Waterman algorithm
T.F. Smith, M.S. Waterman (1981)
Identification of Common Molecular Subsequences
Journal of Molecular Biology 147: 195-197
[PubMed]

Needleman & Wunsch algorithm
S.B. Needleman & C.D. Wunsch (1970)
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
J. Mol. Biol. (1970) 48, 443-453
[PubMed]

Blast 2 Sequences
T.A. Tatusova & T.L. Madden (1999)
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
FEMS Microbiol Lett. 1999 May 15;174(2):247-50.
[PubMed]

jFatCat
Author: Andreas Prlić. The 3D alignment program is based on FATCAT, BioJava and Jmol.
Yuzhen Ye & Adam Godzik (2003)
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Bioinformatics vol.19 suppl. 2. ii246-ii255.
[PubMed] [more]

R.C.G. Holland; T. Down; M. Pocock; A. Prlić; D. Huen; K. James; S. Foisy; A. Dräger; A. Yates; M. Heuer; M.J. Schreiber (2008)
BioJava: an Open-Source Framework for Bioinformatics
Bioinformatics 2008 24(18):2096-2097
[PubMed]

jCE
Author: Andreas Prlić. The 3D alignment program is based on CE, BioJava and Jmol.
Shindyalov IN, Bourne PE (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Eng 11: 739-747
[PubMed] [pdf]

External Structure Alignment Servers:

FATCAT website
Y. Ye & A. Godzik.
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
2003. Bioinformatics vol.19 suppl. 2. ii246-ii255.
[PubMed] [more]

Dali website
L. Holm & J. Park (2000)
DaliLite workbench for protein structure comparison.
Bioinformatics 16, 566-567.
[PubMed]

TopMatch website
M.J. Sippl & M. Wiederstein (2008)
A note on difficult structure alignment problems.
Bioinformatics 24, 426-427
[PubMed]
M.J. Sippl (2008)
On distance and similarity in fold space.
Bioinformatics 24, 872-873.
[PubMed]

TM-Align website
Y. Zhang & J. Skolnick (2005)
TM-align: A protein structure alignment algorithm based on TM-score
Nucleic Acids Research, 2005 33: 2302-2309
[PubMed]

Mammoth website
A. Ortiz, C.E.M. Strauss, O. Olmea (2002)
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
Protein Sci. 2002 Nov;11(11):2606-21.
[PubMed]

An Information Portal to Biological Macromolecular Structures

Print Options:

RCSB PDB Protein Comparison Tool

Acknowledgements