Secondary Structure Assignment

Structural Bioinformatics

Volumn , Issue , 2005, Pages 339-363

  Andersen, Claus A F ^a,b   Rost, Burkhard ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Dictionary of secondary structure of proteins (DSSP); Regular macroelements; Secondary structure assignments

Indexed keywords

MACRO ELEMENT; SECONDARY STRUCTURE OF PROTEINS; SECONDARY STRUCTURES;

EID: 84872269680     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471721204.ch17     Document Type: Chapter

References (89)

1. Andersen CAF (2001): Protein structure and the diversity of hydrogen bonds. The Technical University of Denmark Ph.D. Thesis.
2. Andersen CAF, Palmer AG, Brunak S, Rost B (2001): Continuous secondary structure assignment correlates with protein flexibility. Structure. [The evaluation criterion for structure assignments based on protein flexibility is described. The relationship between variations in NMR model coordinates and protein motion is demonstrated. The influence of motion on secondary structure is analyzed and an estimate for the upper limit of secondary structure prediction is presented.]
3. Baker EN, Hubbard RE (1984): Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44:97-179.
4. Baldi P, Brunak S, Frasconi P, Soda G, Pollastri G (1999): Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15:937-46.
5. Barton GJ (1995): Protein secondary structure prediction. Curr Opin Struct Biol 5:372-6.
6. Berman HM, Westbrook J, Feng Z, Gillliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000): The Protein Data Bank. Nucleic Acids Res 28:235-42.
7. Blundell TL, Mizuguchi K (2000): Structural genomics: an overview. Prog Biophys Mol Biol 73:289-95.
8. Boobbyer DN, Goodford PJ, McWhinnie PM, Wade RC (1989): New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem 32:1083-94.
9. Bordo D, Argos P (1994): The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins. J Mol Biol 243:504-19.
10. Brändén C, Tooze J (1991): Introduction to Protein Structure. New York: Garland Publishing.
11. Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T, Lin D, Sali A, Studier FW, Swaminathan S (1999): Structural genomics: beyond the human genome project. Nat Genet 23:151-7.
12. Bystroff C, Baker D (1998): Prediction of local structure in proteins using a library of sequencestructure motifs. J Mol Biol 281:565-77.
13. Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon J-P (1993): Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng 6:377-82. [A statistical comparison of secondary structure assignments between DSSP, P-Curve, and DEFINE is presented. The CF and GOR prediction algorithms are furthermore compared to the committee of the three assignment schemes analyzed.]
14. Creighton T (1993): Proteins: Structures and Molecular Properties. New York: W.H. Freeman.
15. Cuff JA, Barton GJ (1999): Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34:508-19.
16. de la Cruz X, Thornton JM (1999): Factors limiting the performance of prediction-based fold recognition methods. Protein Sci 8:750-9.
17. Di Francesco V, Munson PJ, Garnier J (1999): FORESST: fold recognition from secondary structure predictions of proteins. Bioinformatics 15:131-40.
18. Eyrich V, Martí-Renom MA, Przybylski D, Fiser A, Pazos F, Valencia A, Sali A, Rost B (2002): EVA: continuous automatic evaluation of protein structure prediction servers. Structure 10:175-84.
19. Fain B, Levitt M (2001): A novel method for sampling alpha-helical protein backbones. J Mol Biol 305:191-201.
20. Fasman GD (1989): The development of the prediction of protein structure. In: Fasman GD, editor. Prediction of Protein Structure and the Principles of Protein Conformation. New York:Plenum Press, pp 193-303.
21. Finkelstein AV (1997): Protein structure: what is it possible to predict now? Curr Opin Struct Biol 7:60-71.
22. Fischer D, Eisenberg D (1996): Fold recognition using sequence-derived properties. Protein Sci 5:947-55.
23. Frishman D, Argos P (1995): Knowledge-based protein secondary structure assignment. Proteins 23:566-79. [The phi-psi statistics used for the α-helix and β-sheet assignments are described along with a visualization of the five β-sheet hydrogen bond conformation used. The data set of 226 protein chains containing the crystallographers' assignments, used as the standardof- truth, is also listed.]
24. Hogue CW, Bryant SH (1998): Structure databases. Methods Biochem Anal 39:46-73.
25. Holm L, Sander C (1998): Touring protein fold space with Dali/FSSP. Nucleic Acids Res 26:318-21.
26. Hvidt A, Westh P (1998): Different views on the stability of protein conformations, and hydrophobic effects. J Solution Chem 27:395-402.
27. Jaroszewski L, Rychlewski L, Zhang B, Godzik A (1998): Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 7:1431-40.
28. Jeffrey GA, Saenger W (1994): Hydrogen Bonding in Biological Structures. Berlin: Springer-Verlag.
29. Jennings AJ, Edge CM, Sternberg MJ (2001): An approach to improving multiple alignments of protein sequences using predicted secondary structure. Protein Eng 14:227-31.
30. Jones DT (1999a) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287:797-815.
31. Jones DT (1999b) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195-202.
32. Jones DT, Orengo CA, Thornton JM (1996): Protein folds and their recognition from sequence. In: Sternberg MJE, editor. Protein Structure Prediction. Oxford: Oxford University Press, pp 173-206.
33. Jones DT, Tress M, Bryson K, Hadley C (1999): Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins 37:104-11.
34. Kabsch W, Sander C (1983a) Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22:2577-637. [The original description of DSSP describes the secondary structure definitions applied and the underlying rationale. The hydrogen bond model is analyzed along with the reasoning behind the chosen energy cutoff.]
35. Kabsch W, Sander C (1983b) How good are predictions of protein secondary structure? FEBS Lett 155:179-82.
36. Kabsch W, Sander C (1983c) Segment83. Unpublished.
37. Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J (1999): A method for the improvement of threading-based protein models. Proteins 37:592-610.
38. Lesk AM (1991): Protein Architecture-A Practical Approach. Oxford: Oxford University Press.
39. Lesk AM, Lo Conte L, Hubbard TJP (2001): Assessment of novel folds targets in CASP4:predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins. 45(5):598-118.
40. Lesk AM, Rose GD (1981): Folding units in globular proteins. Proc Natl Acad Sci USA 78:4304-8.
41. Lindahl E, Elofsson A (2000): Identification of related proteins on family, superfamily and fold level. J Mol Biol 295:613-25.
42. Liu J, Rost B (2001a) Comparing function and structure between entire proteomes. Protein Sci 10:1970-9.
43. Liu J, Rost B (2001b) Target space for structural genomics revisited. Bioinformatics. 18:922-33.
44. Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C (2000): SCOP: a structural classification of proteins database. Nucleic Acids Res 28:257-9.
45. Lupas A (1996): Coiled coils: new structures and new functions. TIBS 21:375-82.
46. Marchler-Bauer A, Addess KJ, Chappey C, Geer L, Madej T, Matsuo Y, Wang Y, Bryant SH (1999): MMDB: Entrez's 3D structure database. Nucleic Acids Res 27:240-3.
47. Marti-Renom MA, Stuart A, Fiser A, Sanchez R, Melo F, Sali A (2000): Comparative protein structure modeling of genes and genomes. Ann Rev Biophys Biomol Struct 29:291-325.
48. Murzin AG (1996): Structural classification of proteins: new superfamilies. Curr Opin Struct Biol 6:386-94.
49. Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM (1999): The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res 27:275-9.
50. Pauling L (1939): The Nature of the Chemical Bond. New York: Cornell University Press.
51. Pauling L, Corey RB (1951): Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc Natl Acad Sci USA 37:729-40.
52. Pauling L, Corey RB, Branson HR (1951): The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205-34.
53. Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA (2001): A rapid classification protocol for the CATH domain database to support structural genomics. Nucleic Acids Res 29:223-7.
54. Przytycka T, Aurora R, Rose GD (1999): A protein taxonomy based on secondary structure. Nat Struct Biol 6:672-82.
55. Quiocho FA, Spurlino JC, Rodseth LE (1997): Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. Structure 5:997.
56. Ramachandran GN, Sasisekharan V (1968): Conformation of polypeptides and proteins. Adv Protein Chem 23:284-438.
57. Rice DW, Eisenberg D (1997): A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol 267:1026-38.
58. Richards FM, Kundrot CE (1988): Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 3:71-84. [The distance matrix masks used are listed for the different secondary structure elements. An overview of the methods for secondary structure assignment is presented.]
59. Richardson JS, Richardson DC (1989): Principles and patterns of protein conformation. In: Fasman GD, editor. Prediction of Protein Structure and the Principles of Protein Conformation. New York: Plenum Press, pp 1-98.
60. Rost B (1995): TOPITS: Threading one-dimensional predictions into three-dimensional structures. In: Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S, editors. Third International Conference on Intelligent Systems for Molecular Biology; Cambridge, England. Menlo Park, CA: AAAI Press, pp 314-21.
61. Rost B (1996): PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 266:525-39.
62. Rost B (1998): Marrying structure and genomics. Structure 6:259-63.
63. Rost B (2001b) Protein secondary structure prediction continues to rise. J Struct Biol 134:204-18.
64. Rost B (2001c) Rising accuracy of protein secondary structure prediction. In: Chasman D, editor. Protein Structure Determination, Analysis, and Modeling for Drug Discovery. New York: Dekker.
65. Rost B, Eyrich V (2001): EVA: large-scale analysis of secondary structure prediction. Proteins. 45(5):S192-S99.
66. Rost B, O'Donoghue SI (1997): Sisyphus and prediction of protein structure. CABIOS 13:345-56.
67. Rost B, Sander C (1994): 1D secondary structure prediction through evolutionary profiles. In:Bohr H, Brunak S, editors. Protein Structure by Distance Analysis. Amsterdam: IOS Press, pp 257-76.
68. Rost B, Sander C (1996): Bridging the protein sequence-structure gap by structure predictions. Ann Rev Biophys Biomol Struct 25:113-36.
69. Rost B, Sander C (2000): Third generation prediction of secondary structure. Methods Mol Biol 143:71-95.
70. Rost B, Schneider R, Sander C (1997): Protein fold recognition by prediction-based threading. J Mol Biol 270:471-80.
71. Russell RB, Copley RR, Barton GJ (1996): Protein fold recognition by mapping predicted secondary structures. J Mol Biol 259:349-65.
72. Sali A (1998): 100,000 protein structures for the biologist. Nat Struct Biol 5:1029-32.
73. Sauder JM, Arthur JW, Dunbrack Jr RL (2000): Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40:6-22.
74. Schulz GE (1988): A critical evaluation of methods for prediction of protein secondary structures. Ann Rev Biophys Biophys Chem 17:1-21, PMID: 329:35-82.
75. Shapiro L, Harris T (2000): Finding function through structural genomics. Curr Opin Biotech 11:31-5.
76. Sippl MJ (1995): Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-35.
77. Sippl MJ, Floeckner H (1996): Threading thrills and threats. Structure 4:15-9.
78. Sklenar H, Etchebest C, Lavery R (1989): Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6:46-60. [The geometrical measures used for the assignment are visualized along with phi-psi plots of the helicoidal parameters. The differences to assignments based on phi-psi angle or hydrogen bond descriptions of secondary structure are also illustrated.]
79. Srinivasan R, Rose GD (1999): A physical basis for protein secondary structure. Proc Natl Acad Sci USA 96:14258-63.
80. Sternberg MJ, Bates PA, Kelley LA, MacCallum RM (1999): Progress in protein structure prediction: assessment of CASP3. Curr Opin Struct Biol 9:368-73.
81. Suugiyama S, Matsuo Y, Maenaka K, Vassylyev DG, Matsushima M, Kashiwagi K, Igarashi K, Morikawa K (1996): The 1.8-°A X-ray structure of the Escherichia coli potd protein complexed with spermidine and the mechanism of polyamine binding. Protein Sci 5:1984-90.
82. Taylor WR (2001): Defining linear segments in protein structure. J Mol Biol 310:1135-50. [STICK finds a set of line segments independently of any external secondary structure definition. This method allows the segments to be used as a novel basis for secondary structure definition by taking the average rise/residue along each axis to characterize the segment. This practice has the advantage that secondary structures are described by a single (continuous) value that is not restricted to the conventional classes of α-helix and β-strand.]
83. Teeter MM (1984): Water structure of a hydrophobic protein at atomic resolution. Pentagon rings of water molecules in crystals of crambin. Proc Natl Acad Sci USA 81:6014.
84. Wade RC, Clark KJ, Goodford PJ (1993): Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J Med Chem 36:140-7.
85. Wilmot CM, Thornton JM (1990): Turns and their distortions: a proposed new nomenclature. Protein Eng 3:479-94.
86. Xu H, Aurora R, Rose GD, White RH (1999a) Identifying two ancient enzymes in Archaea using predicted secondary structure alignment. Nat Struct Biol 6:750-4.
87. Xu Y, Xu D, Crawford OH, Einstein J, Jr, Larimer F, Uberbacher E, Unseren MA, Zhang G (1999b) Protein threading by PROSPECT: a prediction experiment in CASP3. Protein Eng 12:899-907.
88. Yang AS, Honig B (2000): 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 301:665-78.
89. Young M, Kirshenbaum K, Dill KA, Highsmith S (1999): Predicting conformational switches in proteins. Protein Sci 8:1752-64. [A data set of 16 protein sequences having functions that involve substantial backbone rearrangements is analyzed with respect to the ambivalence of predicted secondary structure. The authors find all segments involved in conformational switches to have ambivalent predictions, measured by the similarity in prediction probabilities for helix, sheet, and loop, as reported by PHD (see Chapter 28).]