RCSB PDB Comparison Tool Reference
Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
Pre-calculated protein structure alignments at the RCSB PDB website
Bioinformatics 26: 2983-2985
[PubMed]
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Smith & Waterman algorithm
T.F. Smith, M.S. Waterman (1981)
Identification of Common Molecular Subsequences
Journal of Molecular Biology 147: 195-197
[PubMed]
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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]
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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]
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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]
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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]
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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]
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Dali website
L. Holm & J. Park (2000)
DaliLite workbench for protein structure comparison.
Bioinformatics 16, 566-567.
[PubMed]
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TopMatch website
M.J. Sippl & M. Wiederstein (2012)
Detection of correlations in protein structures and molecular complexes.
Structure 20, 718-728.
[PubMed]
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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]
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