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[30]
Remington SJ, Matthews BW. A general method to assess similarity of protein structures, with
applications to T4 bacteriophage lysozyme. Proc Natl Acad Sci U S A 1978;75 (5):2180-4.
[31]
Levine M, Stuart D, Williams J. A method for the systematic comparison of the three-dimensional
structures of proteins and some results. Acta Cryst. 1984;A40:600-10.
[32]
Karpen ME, de Haseth PL, Neet KE. Comparing short protein substructures by a method based on
backbone torsion angles. Proteins 1989;6 (2):155-67.
[33]
Rackovsky S. Quantitative organization of the known protein x-ray structures. I. Methods and short-
length-scale results. Proteins 1990;7 (4):378-402.
[34]
Rackovsky S, Scheraga HA. Influence of ordered backbone structure on protein folding. A study of
some simple models. Macromolecules 1978;11 (1):1-8.
[35]
Orengo CA. A review of methods for protein structure comparison. In: Taylor WR, editor. Patterns
in Protein Sequence and Structure. Heidelberg: Springer-Verlag, 1992. pp. 159-88.
[36]
De Brevern AG, Benros C, Gautier R, Valadie H, Hazout S, Etchebest C. Local backbone structure
prediction of proteins. In Silico Biol 2004;4 (2):0031.
[37]
de Brevern AG, Valadie H, Hazout S, Etchebest C. Extension of a local backbone description using a
structural alphabet: a new approach to the sequence-structure relationship. Protein Sci 2002;11
(12):2871-86.
[38]
Camproux AC, Gautier R, Tuffery P. A hidden markov model derived structural alphabet for
proteins. J Mol Biol 2004;339 (3):591-605.
[39]
Guyon F, Camproux AC, Hochez J, Tuffery P. SA-Search: a web tool for protein structure mining
based on a Structural Alphabet. Nucleic Acids Res 2004;32 (Web Server issue):W545-8.
[40]
Taylor WR, Orengo CA. Protein structure alignment. J Mol Biol 1989;208 (1):1-22.
[41]
Orengo CA, Brown NP, Taylor WR. Fast structure alignment for protein databank searching.
Proteins 1992;14 (2):139-67.
[42]
Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol
1993;233 (1):123-38.
[43]
Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure
comparison. Proc Natl Acad Sci U S A 1998;95 (11):5913-20.
[44]
Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP. Comparison of three algorithms for the
assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein
Eng 1993;6 (4):377-82.
[45]
Andersen CA, Bohr H, Brunak S. Protein secondary structure: category assignment and
predictability. FEBS Lett 2001;507 (1):6-10.
[46]
Andersen CA, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein
flexibility. Structure (Camb) 2002;10 (2):175-84.
[47]
Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and
structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J
Mol Biol 2000;301 (3):665-78.
[48]
Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and
structures. II. On the relationship between sequence and structural similarity for proteins that are not
obviously related in sequence. J Mol Biol 2000;301 (3):679-89.
[49]
Yang AS, Honig B. An integrated approach to the analysis and modeling of protein sequences and
structures. III. A comparative study of sequence conservation in protein structural families using
multiple structural alignments. J Mol Biol 2000;301 (3):691-711.
[50]
Alexandrov NN, Fischer D. Analysis of topological and nontopological structural similarities in the
PDB: new examples with old structures. Proteins 1996;25 (3):354-65.
[51]
Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data:
secondary structure and first-level supersecondary structure. Proteins 1988;3 (2):71-84.
[52]
Mizuguchi K, Go N. Comparison of spatial arrangements of secondary structural elements in
proteins. Protein Eng 1995;8 (4):353-62.
[53]
Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995;23 (3):356-69.
[54]
Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct
Biol 1996;6 (3):377-85.
[55]
Martin AC. The ups and downs of protein topology; rapid comparison of protein structure. Protein
Eng 2000;13 (12):829-37.
[56]
Murthy MR. A fast method of comparing protein structures. FEBS Lett 1984;168 (1):97-102.
[57]
Mitchell EM, Artymiuk PJ, Rice DW, Willett P. Use of techniques derived from graph theory to
compare secondary structure motifs in proteins. J Mol Biol 1990;212 (1):151-66.
[58]
Grindley HM, Artymiuk PJ, Rice DW, Willett P. Identification of tertiary structure resemblance in
proteins using a maximal common subgraph isomorphism algorithm. J Mol Biol 1993;229 (3):707-
21.
