Local protein structures

Current Bioinformatics

Volumn 2, Issue 3, 2007, Pages 165-202

  Offmann, Bernard ^a   Tyagi, Manoj ^a,c   de Brevern, Akexandre G ^b  

^a UNIVERSITÉ DE LA RÉUNION   (France)

^b INSERM   (France)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Ab initio; Molecular modeling; Protein blocks; Protein folds; Secondary structure; Structural alphabet; Structure sequence relationship

Indexed keywords

AB INITIO; LOCAL PROTEIN STRUCTURES; PROTEIN BACKBONE; PROTEIN BLOCK; PROTEIN FOLD; PROTEINS STRUCTURES; SECONDARY STRUCTURES; SIMPLE++; STRUCTURAL ALPHABET; STRUCTURE-SEQUENCE RELATIONSHIP;

PROTEINS;

EID: 41149162869     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489307781662105     Document Type: Article

References (420)

1. Eisenberg D. The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins. Proc Natl Acad Sci USA 2003; 100: 11207-11210.
2. Rath VL, Ammirati M, Danley DE, et al. Human liver glycogen phosphorylase inhibitors bind at a new allosteric site. Chem Biol 2000; 7: 677-682.
3. Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
4. Pauling L, Corey RB, Branson HR. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1951; 37: 205-211.
5. Pauling L, Corey RB. The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci USA 1951; 37: 251-256.
6. Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995; 20: 374.
7. Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996; 14: 51-5, 29-32.
8. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996; 14: 33-8, 27-28.
9. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536-540.
10. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure 1997; 5: 1093-1108.
11. Rost B. Review: protein secondary structure prediction continues to rise. J Struct Biol 2001; 134: 204-218.
12. Marin A, Pothier J, Zimmermann K, Gibrat JF. FROST: a filter-based fold recognition method. Proteins 2002; 49: 493-509.
13. Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999; Suppl 3: 171-176.
14. Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods Enzymol 2004; 383: 66-93.
15. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 1958; 181: 662-666.
16. Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science 1988; 240: 1648-1652.
17. Pal L, Chakrabarti P, Basu G. Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation. J Mol Biol 2003; 326: 273-291.
18. Presta LG, Rose GD. Helix signals in proteins. Science 1988; 240: 1632-1641.
19. Aurora R, Srinivasan R, Rose GD. Rules for alpha-helix termination by glycine. Science 1994; 264: 1126-1130.
20. Aurora R, Rose GD. Helix capping. Protein Sci 1998; 7: 21-38.
21. Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978; 17: 4277-4285.
22. Imai K, Mitaku S. Mechanisms of secondary structure breakers in soluble proteins. Biophysics 2005; 1: 55-65.
23. Ho BK, Thomas A, Brasseur R. Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. Protein Sci 2003; 12: 2508-2522.
24. Ermolenko DN, Thomas ST, Aurora R, Gronenborn AM, Makha-tadze GI. Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices. J Mol Biol 2002; 322: 123-135.
25. Prieto J, Serrano L. C-capping and helix stability: the Pro C-capping motif. J Mol Biol 1997; 274: 276-288.
26. Dirr HW, Little T, Kuhnert DC, Sayed Y. A conserved N-capping motif contributes significantly to the stabilization and dynamics of the C-terminal region of class Alpha glutathione S-transferases. J Biol Chem 2005; 280: 19480-19487.
27. Kuhnert DC, Sayed Y, Mosebi S, Sayed M, Sewell T, Dirr HW. Tertiary interactions stabilise the C-terminal region of human glu-tathione transferase A1-1: a crystallographic and calorimetric study. J Mol Biol 2005; 349: 825-838.
28. Penel S, Morrison RG, Dobson PD, Mortishire-Smith RJ, Doig AJ. Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings. Protein Eng 2003; 16: 957-961.
29. Regan L. Protein structure. Born to be beta. Curr Biol 1994; 4: 656-658.
30. Colloc N, Cohen FE. Beta-breakers: an a periodic secondary structure. J Mol Biol 1991; 221: 603-613.
31. Zaremba SM, Gregoret LM. Context-dependence of amino acid residue pairing in antiparallel beta-sheets. J Mol Biol 1999; 291: 463-479.
32. Merkel JS, Regan L. Aromatic rescue of glycine in beta sheets. Fold Des 1998; 3: 449-455.
33. Merkel JS, Sturtevant JM, Regan L. Sidechain interactions in parallel beta sheets: the energetics of cross-strand pairings. Stru Fold Des 1999; 7: 1333-1343.
34. Wouters MA, Curmi PM. An analysis of side chain interactions and pair correlations within anti parallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs. Proteins 1995; 22: 119-31.
35. Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN. Determinants of strand register in antiparallel beta-sheets of proteins. Protein Sci 1998; 7: 2287-2300.
36. Mandel-Gutfreund Y, Zaremba SM, Gregoret LM. Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands. J Mol Biol 2001; 305: 1145-1159.
37. Lacroix E, Kortemme T, Lopez de la Paz M, Serrano L. The design of linear peptides that fold as monomeric beta-sheet structures. Curr Opin Struct Biol 1999; 9: 487-93.
38. Dooley CT, Chung NN, Wilkes BC, Schiller PW, Bidlack JM, Pasternak GW, Houghten RA. An all D-amino acid opioid peptide with central analgesic activity from a combinatorial library. Science 1994; 266: 2019-2022.
39. West MW, Wang W, Patterson J, Mancias JD, Beasley JR, Hecht MH. De novo amyloid proteins from designed combinatorial libraries. Proc Natl Acad Sci USA 1999; 96: 11211-11216.
40. Perez-Paya E, Houghten RA, Blondelle SE. Functionalized protein like structures from conformationally defined synthetic combinatorial libraries. J Biol Chem 1996; 271: 4120-4126.
41. Pastor MT, Perez-Paya E. Combinatorial chemistry of beta-hairpins. Mol Divers 2003; 6: 149-155.
42. Ho BK, Curmi PM. Twist and shear in beta-sheets and beta-ribbons. J Mol Biol 2002; 317: 291-308.
43. Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978; 120: 97-120.
44. Robson B, Suzuki E. Conformational properties of amino acid residues in globular proteins. J Mol Biol 1976; 107: 327-356.
45. Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 1974; 13: 211-222.
46. Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry 1974; 13: 222-245.
47. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999; 292: 195-202.
48. Pollastri G, McLysaght A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 2005; 21: 1719-1720.
49. Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002; 47: 228-235.
50. Dor O, Zhou Y. Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins 2006; 66: 838-845.
51. Martin J, Gibrat JF, Rodolphe F. Analysis of an optimal hidden Markov model for secondary structure prediction. BMC Struct Biol 2006; 6: 25.
52. Donohue J. Hydrogen bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1953; 39: 470-478.
53. Pal L, Basu G. Novel protein structural motifs containing two-turn and longer 3(10)-helices. Protein Eng 1999; 12: 811-814.
54. Pal L, Basu G, Chakrabarti P. Variants of 3(10)-helices in proteins. Proteins 2002; 48: 571-579.
55. Baker EN, Hubbard RE. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 1984; 44: 97-179.
56. Barlow DJ, Thornton JM. Helix geometry in proteins. J Mol Biol 1988; 201: 601-619.
57. Karpen ME, de Haseth PL, Neet KE. Differences in the amino acid distributions of 3(10)-helices and alpha-helices. Protein Sci 1992; 1: 1333-1342.
58. Pal L, Dasgupta B, Chakrabarti P. 3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation. Biopolymers 2005; 78: 147-162.
59. Low BW, Baybutt RB. The 7i-helix-A hydrogen bonded configuration of the polypeptide chain. J Am Chem Soc 1952; 74: 5806.
60. Low BW, Greenville-Wells HJ. Generalized mathematical relationships for polypeptide chain helices. The coordinates of the 7i-helix. Proc Natl Acad Sci USA 1953; 39: 785-801.
61. Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968; 23: 283-438.
62. Rohl CA, Doig AJ. Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides. Protein Sci 1996; 5: 1687-1696.
63. Fodje MN, Al-Karadaghi S. Occurrence, conformational features and amino acid propensities for the pi-helix. Protein Eng 2002; 15: 353-358.
64. Weaver TM. The pi-helix translates structure into function. Protein Sci 2000; 9: 201-206.
65. Lee KH, Benson DR, Kuczera K. Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides. Biochemistry 2000; 39: 13737-13747.
66. Millhauser GL. Views of helical peptides: a proposal for the position of 3(10)-helix along the thermodynamic folding pathway. Biochemistry 1995; 34: 3873-3877.
67. Millhauser GL, Stenland CJ, Bolin KA, van de Ven FJ. Local helix content in an alanine-rich peptide as determined by the complete set of 3JHN alpha coupling constants. J Biomol NMR 1996; 7: 331-334.
68. Armen R, Alonso DO, Daggett V. The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions. Protein Sci 2003; 12: 1145-1157.
69. Eswar N, Ramakrishnan C, Srinivasan N. Stranded in isolation: structural role of isolated extended strands in proteins. Protein Eng 2003; 16: 331-339.
70. Cartailler JP, Luecke H. Structural and functional characterization of pi bulges and other short intrahelical deformations. Structure (Camb) 2004; 12: 133-144.
71. Duneau JP, Genest D, Genest M. Detailed description of an alpha helix-->pi bulge transition detected by molecular dynamics simulations of the p185c-erbB2 V659G transmembrane domain. J Biomol Struct Dyn 1996; 13: 753-769.
72. Aller P, Voiry L, Garnier N, Genest M. Molecular dynamics (MD) investigations of preformed structures of the transmembrane domain of the oncogenic Neu receptor dimer in a DMPC bilayer. Biopolymers 2005; 77: 184-197.
73. Sajot N, Genest M. Structure prediction of the dimeric neu/ErbB-2 transmembrane domain from multi-nanosecond molecular dynamics simulations. Eur Biophys J 2000; 28: 648-662.
74. Goetz M, Carlotti C, Bontems F, Dufourc EJ. Evidence for an alpha-helix--> pi-bulge helicity modulation for the neu/erbB-2 membrane-spanning segment. A 1H NMR and circular dichroism study. Biochemistry 2001; 40: 6534-6540.
75. Keefe LJ, Sondek J, Shortle D, Lattman EE. The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease. Proc Natl Acad Sci USA 1993; 90: 3275-3279.
76. Sarma GN, Nickel C, Rahlfs S, Fischer M, Becker K, Karplus PA. Crystal structure of a novel Plasmodium falciparum 1-Cys perox-iredoxin. J Mol Biol 2005; 346: 1021-1034.
77. Fowler CB, Pogozheva ID, LeVine H, Mosberg HI. Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites. Biochemistry 2004; 43: 8700-8710.
78. Love WE, Klock PA, Lattman EE, Padlan EA, Ward KB, Jr., Hen-drickson WA. The structures of lamprey and bloodworm hemoglobins in relation to their evolution and function. Cold Spring Harb Symp Quant Biol 1972; 36: 349-357.
79. Piela L, Nemethy G, Scheraga HA. Proline-induced constraints in alpha-helices. Biopolymers 1987; 26: 1587-600.
80. Blundell T, Barlow D, Borkakoti N, Thornton J. Solvent-induced distortions and the curvature of alpha-helices. Nature 1983; 306: 281-283.
81. Chakrabarti P, Bernard M, Rees DC. Peptide-bond distortions and the curvature of alpha-helices. Biopolymers 1986; 25: 1087-1093.
82. Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data: secondary structure and first-level super-secondary structure. Proteins 1988; 3: 71-84.
83. Kumar S, Bansal M. Structural and sequence characteristics of long alpha helices in globular proteins. Biophys J 1996; 71: 1574-1586.
84. Martin J, Letellier G, Marin A, Taly J-F, de Brevern AG, Gibrat J-F. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. submitted.
85. Kumar S, Bansal M. Geometrical and sequence characteristics of alpha-helices in globular proteins. Biophys J 1998; 75: 1935-1944.
86. Bansal M, Kumar S, Velavan R. HELANAL: a program to characterize helix geometry in proteins. J Biomol Struct Dyn 2000; 17: 811-819.
87. Richardson JS, Getzoff ED, Richardson DC. The beta bulge: a common small unit of nonrepetitive protein structure. Proc Natl Acad Sci USA 1978; 75: 2574-2578.
88. Milner-White EJ. Beta-bulges within loops as recurring features of protein structure. Biochim Biophys Acta 1987; 911: 261-265.
89. Chan AW, Hutchinson EG, Harris D, Thornton JM. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci 1993; 2: 1574-1590.
90. Sondek J, Shortle D. Accommodation of single amino acid insertions by the native state of staphylococcal nuclease. Proteins 1990; 7: 299-305.
91. Sondek J, Shortle D. Structural and energetic differences between insertions and substitutions in staphylococcal nuclease. Proteins 1992; 13: 132-140.
92. Chen PY, Gopalacushina BG, Yang CC, Chan SI, Evans PA. The role of a beta-bulge in the folding of the beta-hairpin structure in ubiquitin. Protein Sci 2001; 10: 2063-2074.
93. Axe DD, Foster NW, Fersht AR. An irregular beta-bulge common to a group of bacterial RNases is an important determinant of stability and function in barnase. J Mol Biol 1999; 286: 1471-1485.
94. Richardson JS, Richardson DC. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci USA 2002; 99: 2754-2759.
95. Siepen JA, Radford SE, Westhead DR. Beta edge strands in protein structure prediction and aggregation. Protein Sci 2003; 12: 2348-2359.
96. Wintjens R, Wodak SJ, Rooman M. Typical interaction patterns in alphabeta and betaalpha turn motifs. Protein Eng 1998; 11: 505-522.
97. Wojcik J, Mornon JP, Chomilier J. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol 1999; 289: 1469-1490.
98. Boutonnet NS, Kajava AV, Rooman MJ. Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins. Proteins 1998; 30: 193-212.
99. Fourrier L, Benros C, de Brevern AG. Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics 2004; 5: 58.
100. Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981; 34: 167-339.
101. Némethy G, Printz MP. The gamma turn, a possible folded conformation of the polypeptide chain. Comparison with the beta turn. Macromolecules 1972; 5: 755-758.
102. Matthews BW. the gamma-turn. Evidence for a new folded conformation in Proteins. Macromolecules 1972; 5: 818-819.
103. Rose GD, Gierasch LM, Smith JA. Turns in peptides and proteins. Adv Protein Chem 1985; 37: 1-109.
104. Milner-White EJ. Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops. J Mol Biol 1988; 199: 503-11.
105. Milner-White EJ. Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites. J Mol Biol 1990; 216: 386-397.
106. Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968; 6: 1425-1436.
107. Lewis PN, Momany FA, Scheraga HA. Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Natl Acad Sci USA 1971; 68: 2293-2297.
108. Kuntz ID. Protein folding. J Am Chem Soc 1972; 94: 4009-4012.
109. Lewis PN, Momany FA, Scheraga HA. Chain reversals in proteins. Biochim Biophys Acta 1973; 303: 211-229.
110. Chou PY, Fasman GD. Beta-turns in proteins. J Mol Biol 1977; 115: 135-175.
111. Rose GD, Seltzer JP. A new algorithm for finding the peptide chain turns in a globular protein. J Mol Biol 1977; 113: 153-164.
112. Rose GD, Wetlaufer DB. The number of turns in globular proteins. Nature 1977; 268: 769-770.
113. Zimmerman SS, Scheraga HA. Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N'-methylamides of Pro-X and X-Pro dipeptides. Biopolymers 1977; 16: 811-843.
114. Wilmot CM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol 1988; 203: 221-232.
115. Wilmot CM, Thornton JM. Beta-turns and their distortions: a proposed new nomenclature. Protein Eng 1990; 3: 479-493.
116. Hutchinson EG, Thornton JM. A revised set of potentials for beta-turn formation in proteins. Protein Sci 1994; 3: 22-16.
117. Hutchinson EG, Thornton JM. PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci 1996; 5: 212-220.
118. Mattos C, Petsko GA, Karplus M. Analysis of two-residue turns in proteins. J Mol Biol 1994; 238: 733747.
119. Kaur H, Raghava GP. An evaluation of beta-turn prediction methods. Bioinformatics 2002; 18: 1508-1514.
120. Kaur H, Raghava GP. BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms. Bioinformatics 2002; 18: 498-499.
121. Kaur H, Raghava GP. BTEVAL: a server for evaluation of beta-turn prediction methods. J Bioinform Comput Biol 2003; 1: 495-504.
122. Kaur H, Raghava GP. Prediction of beta-turns in proteins from multiple alignment using neural network. Protein Sci 2003; 12: 627-634.
123. Kaur H, Raghava GP. A neural network method for prediction of beta-turn types in proteins using evolutionary information. Bioin-formatics 2004; 20: 2751-2758.
124. Fuchs PF, Alix AJ. High accuracy prediction of beta-turns and their types using propensities and multiple alignments. Proteins 2005; 59: 828-839.
125. Zhang Q, Yoon S, Welsh WJ. Improved method for predicting beta-turn using support vector machine. Bioinformatics 2005; 21: 2370-2374.
126. Pham TH, Satou K, Ho TB. Support vector machines for prediction and analysis of beta and gamma-turns in proteins. J Bioinform Comput Biol 2005; 3: 343-358.
127. Ramakrishnan C, Srinivasan N, Nataraj DV. Motifs and conforma-tional analysis of amino acid residues adjoining beta-turns in proteins. Int J Pept Protein Res 1996; 48: 420-428.
128. Guruprasad K, Rajkumar S. Beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials. J Biosci 2000; 25: 143-156.
129. Guruprasad K, Prasad MS, Kumar GR. Analysis of gammabeta, betagamma, gammagamma, betabeta continuous turns in proteins. J Pept Res 2001; 57: 292-300.
130. Guruprasad K, Prasad MS, Kumar GR. Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins. J Pept Res 2000; 56: 250-263.
131. Guruprasad K, Rao MJ, Adindla S, Guruprasad L. Combinations of turns in proteins. J Pept Res 2003; 62: 167-74.
132. Chou KC. Prediction of tight turns and their types in proteins. Anal Biochem 2000; 286: 1-16.
133. Nataraj D, Srinivasan N, Sowdhamini R, Ramakrishnan C. Alpha-turns in protein structures. Curr Sci 1995; 69: 434-447.
134. Pavone V, Gaeta G, Lombardi A, et al. Discovering protein secondary structures: classification and description of isolated alpha-turns. Biopolymers 1996; 38: 705-721.
135. Ramakrishnan C, Nataraj DV. Energy minimization studies on alpha-turns. J Pept Sci 1998; 4: 239-252.
136. Rajashankar KR, Ramakumar S. Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence. Protein Sci 1996; 5: 932-946.
137. Artymiuk PJ, Blake CC, Sippel AE. Genes pieced together--exons delineate homologous structures of diverged lysozymes. Nature 1981; 290: 287-288.
138. Baker EN. Structure of azurin from Alcaligenes denitrificans refinement at 1.8 Å resolution and comparison of the two crystal-lographically independent molecules. J Mol Biol 1988; 203: 1071-1095.
139. Stout CD. Refinement of the 7 Fe ferredoxin from Azotobacter vinelandii at 1.9 Å resolution. J Mol Biol 1989; 205: 545-555.
140. Zanotti G, Wieland T, Benedetti E, Di Blasio B, Pavone V, Pedone C. Structure-toxicity relationships in the amatoxin series. Synthesis of S-deoxy[gamma(R)-hydroxy-Ile3]-amaninamide, its crystal and molecular structure and inhibitory efficiency. Int J Pept Protein Res 1989; 34: 222-228.
141. Wang JH, Yan YW, Garrett TP, et al. Atomic structure of a fragment of human CD4 containing two immunoglobulin-like domains. Nature 1990; 348: 411-418.
142. Chou KC. Prediction and classification of alpha-turn types. Bio-polymers 1997; 42: 837-853.
143. Dasgupta B, Pal L, Basu G, Chakrabarti P. Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding. Proteins 2004; 55: 305-315.
144. Pauling L, Corey RB. The structure of fibrous proteins of the collagen-gelatin group. Proc Natl Acad Sci USA 1951; 37: 272-281.
145. Cowan PM, McGavin S, North AC. The polypeptide chain configuration of collagen. Nature 1955; 176: 1062-1064.
146. Makowska J, Rodziewicz-Motowidlo S, Baginska K, et al. Poly-proline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc Natl Acad Sci USA 2006; 103: 1744-1749
147. Vlasov PK, Kilosanidze GT, Ukrainskii DL, Kuzmin AV, Tuma-nian VG, Esipova NG. Left-handed helix conformation of poly-L-proline II type in globular proteins. Statistics of incidence and a role of sequence. Biofizika 2001; 46: 573-576.
148. Fleming PJ, Fitzkee NC, Mezei M, Srinivasan R, Rose GD. A novel method reveals that solvent water favors polyproline II over beta-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA). Protein Sci 2005; 14: 111-118.
149. Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG, Miller AF, Creamer TP. Host-guest study of left-handed poly-proline II helix formation. Biochemistry 2001; 40: 14376-14383.
150. Cubellis MV, Caillez F, Blundell TL, Lovell SC. Properties of polyproline II, a secondary structure element implicated in protein-protein interactions. Proteins 2005; 58: 880-892.
151. Chen K, Liu Z, Zhou C, Shi Z, Kallenbach NR. Neighbor effect on PPII conformation in alanine peptides. J Am Chem Soc 2005; 127: 10146-10147.
152. Pappu RV, Rose GD. A simple model for polyproline II structure in unfolded states of alanine-based peptides. Protein Sci 2002; 11: 2437-2455.
153. Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR. Poly-proline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 2002; 99: 9190-9195.
154. Mezei M, Fleming PJ, Srinivasan R, Rose GD. Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins 2004; 55: 502-507.
155. Adzhubei AA, Sternberg MJ. Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 1993; 229: 472-493.
156. Creamer TP. Left-handed polyproline II helix formation is (very) locally driven. Proteins 1998; 33: 218-226.
157. Stapley BJ, Creamer TP. A survey of left-handed polyproline II helices. Protein Sci 1999; 8: 587-595.
158. Creamer TP, Campbell MN. Determinants of the polyproline II helix from modeling studies. Adv Protein Chem 2002; 62: 263-282.
159. Chellgren BW, Creamer TP. Short sequences of non-proline residues can adopt the polyproline II helical conformation. Biochemistry 2004; 43: 5864-5869.
160. Chellgren BW, Miller AF, Creamer TP. Evidence for polyproline II helical structure in short polyglutamine tracts. J Mol Biol 2006; 361: 362-371.
161. Whittington SJ, Creamer TP. Salt bridges do not stabilize poly-proline II helices. Biochemistry 2003; 42: 14690-14695.
162. Liu Z, Chen K, Ng A, Shi Z, Woody RW, Kallenbach NR. Solvent dependence of PII conformation in model alanine peptides. J Am Chem Soc 2004; 126: 15141-15150.
163. Berisio R, Loguercio S, De Simone A, Zagari A, Vitagliano L. Polyproline helices in protein structures: A statistical survey. Protein Pept Lett 2006; 13: 847-854.
164. Blanch EW, Morozova-Roche LA, Cochran DA, Doig AJ, Hecht L, Barron LD. Is polyproline II helix the killer conformation? A Raman optical activity study of the amyloidogenic prefibrillar intermediate of human lysozyme. J Mol Biol 2000; 301: 553-563.
165. Eker F, Griebenow K, Schweitzer-Stenner R. Abeta(1-28) fragment of the amyloid peptide predominantly adopts a polyproline II conformation in an acidic solution. Biochemistry 2004; 43: 6893-6898.
166. Hicks JM, Hsu VL. The extended left-handed helix: a simple nucleic acid-binding motif. Proteins 2004; 55: 330-338.
167. Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proc Natl Acad Sci USA 2005; 102: 11698-11703.
168. Thornton JM, Sibanda BL, Edwards MS, Barlow DJ. Analysis, design and modification of loop regions in proteins. Bioessays 1988; 8: 63-69.
169. Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature 1985; 316: 170-174.
170. Milner-White EJ, Poet R. Four classes of beta-hairpins in proteins. Biochem J 1986; 240: 289-292.
171. Sibanda BL, Blundell TL, Thornton JM. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 1989; 206: 759-777.
172. Sibanda BL, Thornton JM. Conformation of beta hairpins in protein structures: classification and diversity in homologous structures. Methods Enzymol 1991; 202: 59-82.
173. Efimov AV. Structure of coiled beta-beta-hairpins and beta-beta-corners. FEBS Lett 1991; 284: 288-92.
174. Ramirez-Alvarado M, Blanco FJ, Niemann H, Serrano L. Role of beta-turn residues in beta-hairpin formation and stability in designed peptides. J Mol Biol 1997; 273: 898-912.
175. Gunasekaran K, Ramakrishnan C, Balaram P. Beta-hairpins in proteins revisited: lessons for de novo design. Protein Eng 1997; 10: 1131-1141.
176. Skelton NJ, Russell S, de Sauvage F, Cochran AG. Amino acid determinants of beta-hairpin conformation in erythropoeitin receptor agonist peptides derived from a phage display library. J Mol Biol 2002; 316: 1111-1125.
177. Sibanda BL, Thornton JM. Accommodating sequence changes in beta-hairpins in proteins. J Mol Biol 1993; 229: 428-447.
178. Blandl T, Cochran AG, Skelton NJ. Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns. Protein Sci 2003; 12: 237-247.
179. Kim J, Brych SR, Lee J, Logan TM, Blaber M. Identification of a key structural element for protein folding within beta-hairpin turns. J Mol Biol 2003; 328: 951-961.
180. Sowdhamini R, Srinivasan N, Ramakrishnan C, Balaram P. Orthogonal beta beta motifs in proteins. J Mol Biol 1992; 223: 845-851.
181. Efimov AV. Structure of alpha-alpha-hairpins with short connections. Protein Eng 1991; 4: 245-250.
182. Efimov AV. Structural similarity between two-layer alpha/beta and beta-proteins. J Mol Biol 1995; 245: 402-415.
183. Engel DE, Degrado WF. alpha-alpha linking motifs and interhelical orientations. Proteins 2005; 61: 325-337.
184. Wintjens RT, Rooman MJ, Wodak SJ. Automatic classification and analysis of alpha alpha-turn motifs in proteins. J Mol Biol 1996; 255: 235-253.
185. Edwards MS, Sternberg JE, Thornton JM. Structural and sequence patterns in the loops of beta alpha beta units. Protein Eng 1987; 1: 173-181.
186. Efimov AV. Super-secondary structures involving triple-strand beta-sheets. FEBS Lett 1993; 334: 253-256.
187. Leszczynski JF, Rose GD. Loops in globular proteins: a novel category of secondary structure. Science 1986; 234: 849-855.
188. Fetrow JS, Horner SR, Oehrl W, Schaak DL, Boose TL, Burton RE. Analysis of the structure and stability of omega loop A replacements in yeast iso-1-cytochrome c. Protein Sci 1997; 6: 197-210.
189. Fetrow JS. Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J 1995; 9: 708-717.
190. Pal M, Dasgupta S. The nature of the turn in omega loops of proteins. Proteins 2003; 51: 591-606.
191. Fetrow JS, Cardillo TS, Sherman F. Deletions and replacements of omega loops in yeast iso-1-cytochrome c. Proteins 1989; 6: 372-381.
192. Krishna MM, Lin Y, Rumbley JN, Englander SW. Cooperative omega loops in cytochrome c: role in folding and function. J Mol Biol 2003; 331: 29-36.
193. Bek E, Berry R. Prohormonal cleavage sites are associated with omega loops. Biochemistry 1990; 29: 178-83.
194. Kishore R, Samuel M, Khan MY, Hand J, Frenz DA, Newman SA. Interaction of the NH2-terminal domain of fibronectin with hepa-rin. Role of the omega-loops of the type I modules. J Biol Chem 1997; 272: 17078-17085.
195. Sanschagrin F, Theriault E, Sabbagh Y, Voyer N, Levesque RC. Combinatorial biochemistry and shuffling of TEM, SHV and Strep-tomyces albus omega loops in PSE-4 class A beta-lactamase. J An-timicrob Chemother 2000; 45: 517-520.
196. Murphy ME, Fetrow JS, Burton RE, Brayer GD. The structure and function of omega loop A replacements in cytochrome c. Protein Sci 1993; 2: 1429-1440.
197. Mulligan-Pullyblank P, Spitzer JS, Gilden BM, Fetrow JS. Loop replacement and random mutagenesis of omega-loop D, residues 70-84, in iso-1-cytochrome c. J Biol Chem 1996; 271: 8633-8645.
198. Sinibaldi F, Piro MC, Howes BD, Smulevich G, Ascoli F, Santucci R. Rupture of the hydrogen bond linking two Omega-loops induces the molten globule state at neutral pH in cytochrome c. Biochemistry 2003; 42: 7604-7610.
199. Berezovsky IN, Grosberg AY, Trifonov EN. Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett 2000; 466: 283-286.
200. Lamarine M, Mornon JP, Berezovsky N, Chomilier J. Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding? Cell Mol Life Sci 2001; 58: 49249-8.
201. Papandreou N, Berezovsky IN, Lopes A, Eliopoulos E, Chomilier J. Universal positions in globular proteins. Eur J Biochem 2004; 271: 4762-4768.
202. Berezovsky IN, Trifonov EN. Loop fold nature of globular proteins. Protein Eng 2001; 14: 403-407.
203. Tramontano A, Chothia C, Lesk AM. Structural determinants of the conformations of medium-sized loops in proteins. Proteins 1989; 6: 382-394.
204. Tramontano A, Lesk AM. Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations. Proteins 1992; 13: 231-245.
205. Rice PA, Goldman A, Steitz TA. A helix-turn-strand structural motif common in alpha-beta proteins. Proteins 1990; 8: 334-340.
206. Ring CS, Kneller DG, Langridge R, Cohen FE. Taxonomy and conformational analysis of loops in proteins. J Mol Biol 1992; 224: 685-699.
207. Ring CS, Cohen FE. Conformational sampling of loop structures using genetic algorithm. Israel J Chem 1994; 34: 245-252.
208. Sun Z, Jiang B. Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank. J Protein Chem 1996; 15: 675-690.
209. Rufino SD, Donate LE, Canard L, Blundell TL. Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures. Pac Symp Biocom-put 1996: 570-589.
210. Donate LE, Rufino SD, Canard LH, Blundell TL. Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction. Protein Sci 1996; 5: 2600-2616.
211. Rufino SD, Donate LE, Canard LH, Blundell TL. Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. J Mol Biol 1997; 267: 352-367.
212. Burke DF, Deane CM. Improved protein loop prediction from sequence alone. Protein Eng 2001; 14: 473-478.
213. Burke DF, Deane CM, Blundell TL. Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. Bioinformatics 2000; 16: 513-519.
214. Geetha V, Munson P, Analysis of linkers of regular secondary structural regions in proteins, In, D. Marshak Eds, Techniques in Protein Chemistry. Academic Press, Orlando, Florida 1997 p. 667-677.
215. Geetha V, Munson PJ. Linkers of secondary structures in proteins. Protein Sci 1997; 6: 2538-2547.
216. Kwasigroch JM, Chomilier J, Mornon JP. A global taxonomy of loops in globular proteins. J Mol Biol 1996; 259: 855-872.
217. Alland C, Moreews F, Boens D, et al. RPBS: a web resource for structural bioinformatics. Nucleic Acids Res 2005; 33: W44-W49.
218. Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ. An automated classification of the structure of protein loops. J Mol Biol 1997; 266: 814-830.
219. Espadaler J, Fernandez-Fuentes N, Hermoso A, et al. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res 2004; 32: D185-D188.
220. Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B. Classification of common functional loops of kinase super-families. Proteins 2004; 56: 539-555.
221. Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJ, Oliva B. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins 2005; 60: 746-757.
222. Espadaler J, Querol E, Aviles FX, Oliva B. Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics 2006; 22: 2237-2243.
223. Li W, Liu Z, Lai L. Protein loops on structurally similar scaffolds: database and conformational analysis. Biopolymers 1999; 49: 481-495.
224. Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997; 25: 231-234.
225. Michalsky E, Goede A, Preissner R. Loops In Proteins (LIP)--a comprehensive loop database for homology modelling. Protein Eng 2003; 16: 979-985.
226. Lesk AM, Introduction to Bioinformatics. 2005, Oxford: Oxford University Press.
227. Schulz GE, Barry CD, Friedman J, Chou PY, Fasman GD, Finkel-stein AV, Lim VI, Pititsyn OB, Kabat EA, Wu TT, Levitt M, Rob-son B, Nagano K. Comparison of predicted and experimentally determined secondary structure of adenyl kinase. Nature 1974; 250: 140-142.
228. Robson B, Garnier J, Introduction to proteins and protein engineering. 1986, Amsterdam: Elsevier Press.
229. Woodcock S, Mornon JP, Henrissat B. Detection of secondary structure elements in proteins by hydrophobic cluster analysis. Protein Eng 1992; 5: 629-635.
230. Levitt M, Greer J. Automatic identification of secondary structure in globular proteins. J Mol Biol 1977; 114: 181-239.
231. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
232. Andersen CA, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein flexibility. Structure (Camb) 2002; 10: 175-184.
233. Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995; 23: 566-579.
234. Bernstein FC, Koetzle TF, Williams GJ, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977; 112: 535-542.
235. Andersen CA, Rost B. Secondary structure assignment. Methods Biochem Anal 2003; 44: 341-363.
236. Andersen CAF, Rost B, Secondary structure assignement, In, P. Bourne Eds, Structural Bioinformatics. 2002 p. 341-364.
237. Carter P, Andersen CA, Rost B. DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res 2003; 31: 3293-3295.
238. Al-Karadaghi S, Cedergren-Zeppezauer ES, Dauter Z, Wilson KS. Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution. Acta Crystallogr D Biol Crystallogr 1995; 51: 805-813.
239. Al-Karadaghi S, Cedergren-Zeppezauer ES, Hovmoller S. Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr 1994; 50: 793-807.
240. Smith D, SSTRUC: A program to calculate a secondary structural summary., in Department of Crystal-lography, Birkbeck College, University of London. 1989.
241. Labesse G, Colloc N, Pothier J, Mornon JP. P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins. Comput Appl Biosci 1997; 13: 291-295.
242. Srinivasan R, Rose GD. A physical basis for protein secondary structure. Proc Natl Acad Sci USA 1999; 96: 14258-14263.
243. Fitzkee NC, Rose GD. Steric restrictions in protein folding: an alpha-helix cannot be followed by a contiguous beta-strand. Protein Sci 2004; 13: 633-639.
244. Fitzkee NC, Fleming PJ, Rose GD. The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDB. Proteins 2005; 58: 852-854.
245. Cubellis MV, Cailliez F, Lovell SC. Secondary structure assignment that accurately reflects physical and evolutionary characteristics. BMC Bioinformatics 2005; 6 Suppl 4: S8.
246. King SM, Johnson WC. Assigning secondary structure from protein coordinate data. Proteins 1999; 35: 313-320.
247. Sklenar H, Etchebest C, Lavery R. Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 1989; 6: 46-60.
248. Dupuis F, Sadoc JF, Mornon JP. Protein secondary structure assignment through Voronoi tessellation. Proteins 2004; 55: 519-528.
249. Dupuis F, Sadoc JF, Jullien R, Angelov B, Mornon JP. Voro3D: 3D Voronoi tessellations applied to protein structures. Bioinformatics 2005; 21: 1715-1716.
250. Taylor T, Rivera M, Wilson G, Vaisman, I. New method for protein secondary structure assignment based on a simple topological descriptor. Proteins 2005; 60: 513-524.
251. Parisien M, Major F. A New Catalog of Protein Beta-Sheets. Proteins 2005: 61: 545-558.
252. Majumdar I, Krishna SS, Grishin NV. PALSSE: A program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics 2005; 6: 202.
253. Colloc 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: 377-382.
254. Sukumar N, Dewanti AR, Mitra B, Mathews FS. High resolution structures of an oxidized and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase. J Biol Chem 2004; 279: 3749-3757.
255. Bornot A, de Brevern AG. Protein beta-turn assignments. Bioinformation 2006; 1: 153-155.
256. de Brevern AG, Benros C, Hazout S, Structural Alphabet: From a Local Point of View to a Global Description of Protein 3D Structures, In, P.V. Yan Eds, Bioinformatics: New Research. Nova Publishers 2005 p. 128-187.
257. Kabsch W, Mannherz HG, Suck D, Pai EF, Holmes KC. Atomic structure of the actin:DNase I complex. Nature 1990; 347: 37-44.
258. Michalopoulos I, Torrance GM, Gilbert DR, Westhead DR. TOPS: an enhanced database of protein structural topology. Nucleic Acids Res 2004; 32: D251-D254.
259. Chothia C, Finkelstein AV. The classification and origins of protein folding patterns. Annu Rev Biochem 1990; 59: 1007-1039.
260. Hutchinson EG, Thornton JM. The Greek key motif: extraction, classification and analysis. Protein Eng 1993; 6: 233-245.
261. Gelly JC, Gracy J, Kaas Q, Le-Nguyen D, Heitz A, Chiche L. The KNOTTIN website and database: a new information system dedicated to the knottin scaffold. Nucleic Acids Res 2004; 32: D156-D159.
262. Lesk AM, Rose GD. Folding units in globular proteins. Proc Natl Acad Sci USA 1981; 78: 4304-4308.
263. Sowdhamini R, Blundell TL. An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci 1995; 4: 506-520.
264. Tsai CJ, Nussinov R. Hydrophobic folding units derived from dissimilar monomer structures and their interactions. Protein Sci 1997; 6: 24-42.
265. Gelly JC, de Brevern AG, Hazout S. 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments. Bioinformatics 2006; 22: 129-133.
266. Gelly JC, Etchebest C, Hazout S, de Brevern AG. Protein Peeling 2: a web server to convert protein structures into series of protein units. Nucleic Acids Res 2006; 34: W75-W78.
267. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998; 281: 565-577.
268. Eisenmesser EZ, Millet O, Labeikovsky W, et al. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005; 438: 117-121.
269. Teague SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2003; 2: 527-541.
270. Raveh B, Rahat O, Basri R, Schreiber G. Rediscovering secondary structures as network motifs--an unsupervised learning approach. Bioinformatics 2007; 23: e163-e169.
271. Benros C, Martin J, Tyagi M, de Brevern AG, Description of the local protein structure. I. Classical approaches, In, A.G. de Brevern Eds, Recent Research Developments in Protein Engineering. Research Signpost, Trivandrum 2007 p. in press.
272. Unger R, Harel D, Wherland S, Sussman JL. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 1989; 5: 355-373.
273. Tuffery P, Guyon F, Derreumaux P. Improved greedy algorithm for protein structure reconstruction. J Comput Chem 2005; 26: 506-513.
274. de Brevern AG, Camproux A-C, Hazout S, Etchebest C, Tuffery P, Protein structural alphabets: beyond the secondary structure description, In, S. Sangadai Eds, Recent Research Developments in Protein Engineering. Research Signpost, Trivandrum 2001 p. 319-331.
275. Karchin R, Evaluating local structure alphabets for protein structure prediction. 2003. p. 301.
276. Tyagi M, Benros C, Martin J, de Brevern AG, Description of the local protein structure. II. Novel approaches., In, A.G. de Brevern Eds, Recent Research Developments in Protein Engineering. Research Signpost, Trivandrum 2007 p. in press.
277. Unger R, Sussman JL. The importance of short structural motifs in protein structure analysis. J Comput Aided Mol Des 1993; 7: 457-472.
278. Prestrelski SJ, Williams AL, Jr., Liebman MN. Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results. Proteins 1992; 14: 430-439.
279. Schuchhardt J, Schneider G, Reichelt J, Schomburg D, Wrede P. Local structural motifs of protein backbones are classified by self-organizing neural networks. Protein Eng 1996; 9: 833-842.
280. Rooman MJ, Rodriguez J, Wodak SJ. Automatic definition of recurrent local structure motifs in proteins. J Mol Biol 1990; 213: 327-336.
281. Fetrow JS, Palumbo MJ, Berg G. Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 1997; 27: 249-271.
282. Camproux AC, Tuffery P, Chevrolat JP, Boisvieux JF, Hazout S. Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng 1999; 12: 1063-1073.
283. Camproux AC, Tuffery P, Buffat L, Andre C, Boisvieux JF, Hazout S. Using short structural building blocks defined by a Hidden Markov Model for analysing patterns between regular secondary structures. Theor Chem Acc 1999; 101(1-3): 33-40.
284. Micheletti C, Seno F, Maritan A. Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies. Proteins 2000; 40: 662-674.
285. de Brevern AG, Etchebest C, Hazout S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 2000; 41: 271-287.
286. Hartigan JA, Wong MA. K-means. Appl Stat 1979; 28: 100-115.
287. Kohonen T. Self-organized formation of topologically correct feature maps. Biol Cybern 1982; 43: 59-69.
288. Kohonen T, Self-Organizing Maps (3rd edition). 2001: Springer. 501.
289. Schneider G, Wrede P. Artificial neural networks for computer-based molecular design. Prog Biophys Mol Biol 1998; 70: 175-222.
290. Rabiner LR. A tutorial on hidden Markov models and selected application in speech recognition. Proceedings of the IEEE 1989; 77: 257-86.
291. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
292. Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Protein Sci 2000; 9: 1753-1773.
293. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000; 29: 291-325.
294. Sali A, Blundell TL. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 1990; 212: 403-428.
295. Jones TA, Thirup S. Using known substructures in protein model building and crystallography. EMBO J 1986; 5: 819-822.
296. Claessens M, Van Cutsem E, Lasters I, Wodak S. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng 1989; 2: 335-345.
297. Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992; 226: 507-533.
298. Du P, Andrec M, Levy RM. Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng 2003; 16: 407-414.
299. Unger R, Harel D, Wherland S, Sussman JL. Analysis of dihedral angles distribution: The doublets distribution determines polypep-tides conformations. Biopolymers 1990; 30: 499-508.
300. Prestrelski SJ, Byler DM, Liebman MN. Generation of a substructure library for the description and classification of protein secondary structure. II. Application to spectra-structure correlations in Fourier transform infrared spectroscopy. Proteins 1992; 14: 440-450.
301. Zhang X, Fetrow JS, Rennie WA, Waltz DL, Berg G. Automatic derivation of substructures yields novel structural building blocks in globular proteins. Proc Int Conf Intell Syst Mol Biol 1993; 1: 438-446.
302. Zhang KY, Fetrow JS, Berg G, Design of an Auto-Associative Neural Network with Hidden Layer Activations that were used to Reclassify Local Protein Structure, In, Eds, Techniques in Protein Chemistry V. Academic Press, Inc 1994 p. 397-404.
303. Sammon J.J.W. A nonlinear mapping for data structure analysis. IEEE Trans Comput 1969; 18: 401-09.
304. Rooman MJ, Rodriguez J, Wodak SJ. Relations between protein sequence and structure and their significance. J Mol Biol 1990; 213: 337-50.
305. Fetrow JS, Berg G. Using information theory to discover side chain rotamer classes: Analysis of the effects of local backbone structure. in Pac Symp Biocomput. 1999.
306. de Brevern AG, Analyse et Prédiction de la structure locale des protéines. 1998, Universite Paris 7-Denis Diderot: Paris. p. 22.
307. Park BH, Levitt M. The complexity and accuracy of discrete state models of protein structure. J Mol Biol 1995; 249: 493-507.
308. Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. J Mol Biol 2002; 323: 297-307.
309. Kolodny R, Levitt M. Protein decoy assembly using short fragments under geometric constraints. Biopolymers 2003; 68: 278-285.
310. Schwartz G. Estimating the dimension of a model. Ann Stat 1978; 6: 461-464.
311. Tuffery P, Derreumaux P. Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm. Proteins 2005; 61(4):732-740.
312. Forcellino F, Derreumaux P. Computer simulations aimed at structure prediction of supersecondary motifs in proteins. Proteins 2001; 45: 159-166.
313. Lazaridis T, Karplus M. Discrimination of the native from mis-folded protein models with an energy function including implicit solvation. J Mol Biol 1999; 288: 477-487.
314. Camproux AC, Tuffery P. Hidden Markov Model-derived structural alphabet for proteins: The learning of protein local shapes captures sequence specificity. Biochim Biophys Acta 2005; 1724: 394-403.
315. Gautier R, Camproux AC, Tuffery P. SCit: web tools for protein side chain conformation analysis. Nucleic Acids Res 2004; 32: W508-W511.
316. Maupetit J, Gautier R, Tuffery P. SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. Nucleic Acids Res 2006; 34: W147-W151.
317. Bonneau R, Strauss CE, Baker D. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins 2001; 43: 1-11.
318. Bonneau R, Tsai J, Ruczinski I, et al. D. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins 2001; Suppl 5: 119-126.
319. Rooman MJ, Wodak SJ. Identification of predictive sequence motifs limited by protein structure data base size. Nature 1988; 335: 45-49.
320. Rooman MJ, Wodak SJ, Thornton JM. Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. Protein Eng 1989; 3: 23-27.
321. Rooman MJ, Wodak SJ. Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins. Proteins 1991; 9: 69-78.
322. Rooman MJ, Wodak SJ. Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins. Biochemistry 1992; 31.
323. Garnier J, Robson B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J Mol Biol 1987; 198: 425-443.
324. Garnier J, Levin JM, Gibrat JF, Biou V. Secondary structure prediction and protein design. Biochem Soc Symp 1990; 57: 11-24.
325. Rooman MJ, Kocher JP, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J Mol Biol 1991; 221: 961-979.
326. Rooman MJ, Kocher JP, Wodak SJ. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry 1992; 31: 10226-10238.
327. Han KF, Baker D. Recurring local sequence motifs in proteins. J Mol Biol 1995; 251: 176-187.
328. Han KF, Baker D. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc Natl Acad Sci USA 1996; 93: 5814-5818.
329. Bystroff C, Simons KT, Han KF, Baker D. Local sequence-structure correlations in proteins. Curr Opin Biotechnol 1996; 7: 417-421.
330. Han KF, Bystroff C, Baker D. Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Sci 1997; 6: 1587-1590.
331. Schneider R, de Daruvar A, Sander C. The HSSP database of protein structure-sequence alignments. Nucleic Acids Res 1997; 25: 226-230.
332. Rost B, Sander C. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci USA 1993; 90: 7558-7562.
333. Rost B, Sander C. Secondary structure prediction of all-helical proteins in two states. Protein Eng 1993; 6: 831-836.
334. Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins 1997; Suppl 1: 167-171.
335. Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J Mol Biol 1998; 283: 293-300.
336. Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 2000; 301: 173-190.
337. de Brevern AG, Nouvelles stratégies d'analyses et de prédiction des structures tridimensionnelles des protéines, in Biology (Analyses de Génomes et Modélisation Moléculaire). 2001, University Paris 7: Paris. p. 208.
338. Chivian D, Kim DE, Malmstrom L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP-6 structures using automated Robetta protocols. Proteins 2005; 61(Suppl 7): 157-166.
339. Bradley P, Chivian D, Meiler J, Misura KM, et al. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins 2003; 53 Suppl 6: 457-468.
340. Chivian D, Robertson T, Bonneau R, Baker D. Ab initio methods. Methods Biochem Anal 2003; 44: 547-557.
341. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003; 302: 1364-1368.
342. Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Accurate computer-based design of a new backbone conformation in the second turn of protein L. J Mol Biol 2002; 315: 471-477.
343. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003; 331: 281-299.
344. Bowers PM, Strauss CE, Baker D. De novo protein structure determination using sparse NMR data. J Biomol NMR 2000; 18: 311-318.
345. Rohl CA, Baker D. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc 2002; 124: 2723-2729.
346. Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004; 55: 656-677.
347. Bystroff C, Shao Y. Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformat-ics 2002; 18 Suppl 1: S54-S61.
348. de Brevern AG. New assessment of Protein Blocks. In Silico Biology 2005; 5: 283-289.
349. 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: 2871-2886.
350. de Brevern AG, Etchebest C, Benros C, Hazout S. Pinning strategy: a novel approach for predicting the backbone structure in terms of Protein Blocks from sequence. J Biosci 2007; 32: 51-72.
351. Etchebest C, Benros C, Hazout S, de Brevern AG. A structural alphabet for local protein structures: Improved prediction methods. Proteins 2005: 810-827.
352. de Brevern AG, Benros C, Gautier R, Valadie H, Hazout S, Etche-best C. Local backbone structure prediction of proteins. In Silico Biol 2004; 4: 381-386.
353. Hunter CG, Subramaniam S. Protein fragment clustering and canonical local shapes. Proteins 2003; 50: 580-588.
354. Hunter CG, Subramaniam S. Protein local structure prediction from sequence. Proteins 2003; 50: 572-579.
355. Sander O, Sommer I, Lengauer T. Local protein structure prediction using discriminative models. BMC Bioinform 2006; 7: 14.
356. Quinlan JR. Induction of decision trees. Machine Learn 1986; 1: 81-106.
357. Schölkopf B, Smola A, Learning with Kernels. 2002, Cambridge, MA: MIT Press.
358. Randomforest. p. [http://cran.r-project.org/src/contrib/Descriptions/randomForest.html].
359. Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins 2003; 51: 504-514.
360. Karplus K, Karchin R, Shackelford G, Hughey R. Calibrating E-values for hidden Markov models with reverse-sequence null models. Bioinformatics 2005; 21(22): 4107-4115.
361. Camproux AC, Gautier R, Tuffery P. A hidden markov model derived structural alphabet for proteins. J Mol Biol 2004; 339: 591-605.
362. Camproux AC, Brevern AG, Hazout S, Tufféry P. Exploring the use of a structural alphabet for structural prediction of protein loops. Theo Chem Acc 2001; 106: 28-35.
363. Regad L, Martin J, Camproux AC. Identification of non random motifs in loops using a structural alphabet. in Computational Intelligence and Bioinformatics and Computational Biology. 2006. Toronto, Canada: IEEE.
364. de Brevern AG, Hazout S. Compacting local protein folds with a hybrid protein model. Theo Chem Acc 2001; 106: 36-47.
365. de Brevern AG, Hazout S. Compactage d'une base de données protéiques recodées dans un alphabet structural. in Secondes Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM) pour la génomique. 2001. Toulouse.
366. Benros C, Hazout S, de Brevern AG. Extension of a local backbone description using a structural alphabet. Hybrid Protein Model: a new clustering approach for 3D local structures. in International Workshop on Bioinformatics ISMIS. 2002. Lyon, France.
367. Benros C, de Brevern AG, Hazout S. Hybrid Protein Model (HPM): A Method For Building A Library Of Overlapping Local Structural Prototypes. Sensitivity Study And Improvements Of The Training. in IEEE Workshop on Neural Networks for Signal Processing. 2003.
368. de Brevern AG, Hazout S. Hybrid protein model' for optimally defining 3D protein structure fragments. Bioinformatics 2003; 19: 345-353.
369. 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: W545-W548.
370. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993; 233: 123-138.
371. Pandini A, Bonati L, Fraternali F, Kleinjung J. MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database. Bioinformatics 2007; 23: 515-516.
372. Tyagi M, Gowri VS, Srinivasan N, de Brevern AG, Offmann B. A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. Proteins 2006; 65: 32-39.
373. Gowri VS, Pandit SB, Karthik PS, Srinivasan N, Balaji S. Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res 2003; 31: 486-488.
374. Pandit SB, Gosar D, Abhiman S, et al. SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes. Nucleic Acids Res 2002; 30: 289-293.
375. Balaji S, Srinivasan N. Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins. Protein Eng 2001; 14: 219-226.
376. Sujatha S, Balaji S, Srinivasan N. PALI: a database of alignments and phylogeny of homologous protein structures. Bioinformatics 2001; 17: 375-376.
377. Balaji S, Sujatha S, Kumar SS, Srinivasan N. PALI-a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res 2001; 29: 61-65.
378. Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, de Brevern AG, Offmann B. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res 2006; 34: W119-W123.
379. Carpentier M, Brouillet S, Pothier J. YAKUSA: a fast structural database scanning method. Proteins 2005; 61: 137-151.
380. Yang JM, Tung CH. Protein structure database search and evolutionary classification. Nucleic Acids Res 2006; 34: 3646-3659.
381. Tung CH, Huang JW, Yang JM. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for fast protein structure database search. Genome Biol 2007; 8: R31.
382. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.
383. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402.
384. Shao Y, Bystroff C. Predicting interresidue contacts using templates and pathways. Proteins 2003; 53 Suppl 6: 497-502.
385. Hou Y, Hsu W, Lee ML, Bystroff C. Remote homolog detection using local sequence-structure correlations. Proteins 2004; 57: 518-530.
386. Yuan X, Bystroff C. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics 2005; 21: 1010-1019.
387. Huang YM, Bystroff C. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformat-ics 2005; 22(4): 413-422.
388. Tsai CJ, Maizel JV, Jr., Nussinov R. Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape. Proc Natl Acad Sci USA 2000; 97: 12038-12043.
389. Tsai CJ, Nussinov R. The building block folding model and the kinetics of protein folding. Protein Eng 2001; 14: 723-733.
390. Tsai HH, Tsai CJ, Ma B, Nussinov R. In silico protein design by combinatorial assembly of protein building blocks. Protein Sci 2004; 13: 2753-2765.
391. Lee I-Y, Soong T-T, Ho J-M, Hwang M-J. Derivation and analysis of fragment librairies of protein structures. in Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04). 2004.
392. Soong T-T, Hwang M-J, Chen C-M. Discovery of recurrent structural motifs for approximating three-dimensional protein structures. J Chinese Chem Soc 2004; 51: 1107-1114.
393. Wang S-L, Chen C-M, Hwang M-J. Classification of protein 3D folds by hidden Markov learning on sequences of structural alphabets. in 3rd Asia Pacific Bioinformatic Conference. 2005. Singapore.
394. Li Z, Brener NE, Iyengar SS, Seetharam G, Dua S, Ramakumar S, Manikandan K, Bahren J. A robust grouping algorithm for clustering of similar protein folding units. in Fourth virtual conference on Genomics and Bioinformatics. 2004.
395. Zhen W-M, Liu X. A protein structural alphabet and its substitution matrix CLESUM. eprint arXiv:q-bio/0412046 2004.
396. Zhen W-M, Liu X. A protein structural alphabet and its substitution matrix CLESUM. in International Conference on Computational Science 2005. 2005. Emory University, Atlanta, USA.
397. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992; 89: 10915-10919.
398. Lin HN, Chang JM, Wu KP, Sung TY, Hsu WL. HYPROSP II--a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. Bioinformatics 2005; 21: 3227-3233.
399. Wu KP, Lin HN, Chang JM, Sung TY, Hsu WL. HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach. Nucleic Acids Res 2004; 32: 5059-5065.
400. Chen C-T, Lin H-N, Wu K-P, Sung T-Y, Hsu W-L. A Knowledge-based Approach to Protein Local Structure Prediction. in Asia Pacific Bioinformatics Conference. 2006. Taipei, Taiwan.
401. Tang TCK, Discovering protein sequence-structure motifs and two applications to structural prediction, in Computer science. 2004, University of Waterloo: Waterloo, Ontario, Canada.
402. Tang TCK, Xu J, Ming L. Discovering protein sequence-structure motifs and two applications to structural prediction. in Pacific Symposium on Biocomputing (PSB'05). 2005.
403. Kuang R, Leslie CS, Yang AS. Protein backbone angle prediction with machine learning approaches. Bioinformatics 2004; 20: 1612-1621.
404. Yang AS, Wang LY. Local structure prediction with local structure-based sequence profiles. Bioinformatics 2003; 19: 1267-1274.
405. Yang AS, Wang LY. Local structure-based sequence profile database for local and global protein structure predictions. Bioinformat-ics 2002; 18: 1650-1657.
406. Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 1984; 81: 1075-1078.
407. Argos P. Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis. J Mol Biol 1987; 197: 331-348.
408. Wilson IA, Haft DH, Getzoff ED, Tainer JA, Lerner RA, Brenner S. Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition. Proc Natl Acad Sci USA 1985; 82: 5255-5259.
409. Benros C, de Brevern AG, Etchebest C, Hazout S. Assessing a novel approach for predicting local 3D protein structures from sequence. Proteins: Structure, Functions and Bioinformatics 2006: 62: 865-880.
410. de Brevern AG, Hazout S. Hybrid Protein Model (HPM): a method to compact protein 3D-structures information and physicochemical properties. IEEE-Computer Society 2000; S1: 49-54.
411. de Brevern AG. Compartimentation chromosomique. Biofutur 2002; 225: 20-22.
412. de Brevern AG, Loirat F, Badel-Chagnon A, Andre C, Vincens P, Hazout S. Genome compartimentation by a hybrid chromosome model (HXM). Application to Saccharomyces cerevisae subte-lomeres. Comput Chem 2002; 26: 437-445.
413. de Brevern AG, Wong H, Tournamille C, Colin Y, Le Van Kim C, Etchebest C. A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC). Bio-chim Biophys Acta 2005; 1724: 288-306.
414. Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Mod 2001; 7: 306-317.
415. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem 2005; 26: 1701-1718.
416. Dudev T, Lin YL, Dudev M, Lim C. First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations. J Am Chem Soc 2003; 125: 3168-3180.
417. Petkovich M, Brand NJ, Krust A, Chambon P. A human retinoic acid receptor which belongs to the family of nuclear receptors. Nature 1987; 330: 444-450.
418. Dudev M, Lim C. Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites. BMC Bioinfor-matics 2007; 8: 212.
419. Matthews B. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975; 405: 442-451.
420. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000; 16: 412-424.