Graphical interpretation of Boolean operators for protein NMR assignments

Journal of Biomolecular NMR

Volumn 42, Issue 1, 2008, Pages 11-21

  Verdegem, Dries ^a   Dijkstra, Klaas ^b   Hanoulle, Xavier ^a   Lippens, Guy ^a  

^a UNIVERSITÉ DES SCIENCES ET TECHNOLOGIES DE LILLE   (France)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Assignmentof structured proteins; Assignmentof unfolded proteins; Boolean operators in NMR; Computer aided sequential assignment; Graphicalsemi automatic protein assignment method

Indexed keywords

CYCLOPHILIN B; TAU PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOANALYSIS; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER PROGRAM; CONTROLLED STUDY; INFORMATION SCIENCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE;

MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 51949094766     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-008-9262-2     Document Type: Article

References (95)

1. 13Cα chemical shifts and their (i,i - 1) sequential connectivities. J Biomol NMR 23:263-270
2. Atreya H, Chary K, Govil G (2000) Automated NMR assignments of proteins for high throughput structure determination: TATAPRO II. Curr Sci 83:1372-1376
3. Atreya H, Sahu S, Chary K, Govil G (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J Biomol NMR 17:125-136
4. Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR (2000) The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparce unassigned NMR data. J Comput Biol 7:537-558
5. Bailey-Kellogg C, Chainraj S, Pandurangan G (2005) A random graph approach to NMR sequential assignment. J Comput Biol 12:569-583
6. Bartels C, Billeter M, Güntert P, Wüthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207-213
7. Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT - a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139-149
8. Bernstein R, Cieslar C, Ross A, Oschkinat H, Freund J, Holak TA (1993) Computer-assisted assignment of multidimensional NMR spectra of proteins: Application to 3D NOESY-HMQC and TOCSY-HMQC spectra. J Biomol NMR 3:245-251
9. Buchler NE, Zuiderweg ER, Wang H, Goldstein RA (1997) Protein heteronuclear NMR assignments using mean-field simulated annealing. J Magn Reson 125:34-42
10. Choy W, BC S, Zhu G (1997) Using neural network predicted secondary structure information in automatic protein NMR assignment. J Chem Inf Comput Sci 37:1086-1094
11. Coggins BE, Zhou P (2003) PACES: Protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93-111
12. Croft D, Kemmink J, Neidig KP, Oschkinat H (1997) Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. J Biomol NMR 10:207-219
13. Eads C, Kuntz I (1989) Programs for computer-assisted sequential assignment of proteins. J Magn Reson 82:467-482
14. Eccles C, Güntert P, Billeter M, Wüthrich K (1991) Efficient analysis of protein 2D NMR spectra using the software package EASY. J Biomol NMR 1:111-130
15. Eghbalnia HR, Bahrami A, Wang L, Assadi A, Markley JL (2005) Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO). J Biomol NMR 32:219-233
16. Friedrichs M, Mueller L, Wittekind M (1994) An automated procedure for the assignment of protein 1HN, 15N, 13C alpha, 1H alpha, 13C beta and 1H beta resonances. J Biomol NMR 4:703-726
17. Goddard T, Kneller D (1989) Sparky 3. University of California, San Francisco
18. 15N edited 3D-NOESY-HSQC spectra using back calculated and experimental spectra. J Magn Reson 137:39-45
19. Grishaev A, Llinás M (2004) BACUS: A Bayesian protocol for the identification of protein NOESY spectra via unassigned spin systems. J Biomol NMR 28:1-10
20. Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS, Sönnichsen FD, Sykes BD (1998) CAMRA: Chemical shift based computer aided protein NMR assignments. J Biomol NMR 12:395-405
21. Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR (2002) Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR 23:271-287
22. Güntert P, Salzmann M, Braun D, Wüthrich K (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR 18:129-137
23. Hanoulle X, Melchior A, Sibille N, Parent B, Denys A, Wieruszeski JM, Horvath D, Allain F, Lippens G, Landrieu I (2007) Structural and functional characterisation of the interaction between cyclophilin B and a heparin derived oligosaccharide. J Biol Chem 282:34148-134158
24. Hare BJ, Prestegard JH (1994) Application of neural networks to automated assignment of NMR spectra in proteins. J Biomol NMR 4:35-46
25. Helgstrand M, Kraulis P, Allard P, Härd T (2000) Ansig for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra. J Biomol NMR 18:329-336
26. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Biomol NMR 319:209-227
27. Herrmann T, Güntert P, Wüthrich K (2002b) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171-189
28. Hitchens T, Lukin JA, Zhan YP, McCallum SA, Rule GS (2003) MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR 25:1-9
29. Hyberts SG, Wagner G (2003) IBIS - A tool for automated sequential assignment of proteins spectra from triple resonance experiments. J Biomol NMR 26:335-344
30. 15N spectra of larger proteins: Heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29:4659-4667
31. Johnson BA, Blevins RA (1994) NMR view: A computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
32. Jung YS, Zweckstetter M (2004) Mars - robust automatic backbone assignment of proteins. J Biomol NMR 30:11-23
33. Kay LE, Ikura M, Tschudin R, Bax A (1990) Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins. J Magn Reson 89:496-514
34. Kjaer M, Andersen K, Poulsen F (1994) Automated and semiautomated analysis of homo- and heteronuclear multidimensional nuclear magnetic resonance spectra of proteins: The program PRONTO. Methods Enzymol 239:288-308
35. 1H NMR spectra of proteins: Basic algorithms and application to phoratoxin B. J Biomol NMR 1:23-47
36. Kobayashi N, Iwahara J, Koshiba S, Tomizawa T, Tochio N, Güntert P, Kigawa T, Yokoyama S (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR studies. J Biomol NMR 39:31-52
37. Kraulis P (1989) ANSIG: A computer program for the assignment of 1H NMR spectra by interactive computer graphics. J Magn Reson 84:627-633
38. Kraulis P (1994) Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach. J Mol Biol 243:696-718
39. Langmead CJ, Donald BR (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR assignments. J Biomol NMR 29:111-138
40. Langmead CJ, Yan A, Lilien R, Wang L, Donald BR (2004) A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. J Comput Biol 11:277-298
41. Leutner M, Gschwind RM, Liermann J, Schwarz C, Gemmecker G, Kessler H (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J Biomol NMR 11:31-43
42. Li KB, Sanctuary B (1996) Automated extracting of amino acid spin systems in proteins using 3D HCCH-COSY/TOCSY spectroscopy and constrained partioning algorithm. J Chem Inf Comput Sci 36:585-593
43. Li KB, Sanctuary B (1997a) Automated resonance assignment of proteins using heteronuclear 3D NMR. 1. Backbone spin systems extraction and creation of polypeptides. J Chem Inf Comput Sci 37:359-366
44. Li KB, Sanctuary B (1997b) Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment. J Chem Inf Comput Sci 37:467-477
45. Lin G, Xiang W, Tegos T, Li Y (2006) Statistical evaluation of NMR backbone resonance assignment. Int J Bioinform Res Appl 2:147-160
46. Lin G, Xu D, Chen ZZ, Jiang T, Wen J, Xu Y (2003) Computational assignment of protein backbone NMR peaks by efficient bounding and filtering. J Bioinform Comput Biol 1:387-409
47. Lin HN, Wu KP, Chang JM, Hsu WL (2005) GANA - a genetic algorithm for NMR backbone resonance assignment. Nucleic Acids Res 33:4593-4601
48. Lukin JA, Gove AP, Talukdar SN, Ho C (1997) Automated probabilistic method for assigning backbone resonances of (13C, 15N)-labeled proteins). J Biomol NMR 9:151-166
49. Malliavin T, Pons J, Delsuc M (1998) An NMR assignment module implemented in the Gifa NMR processing program. Bioinformatics 14:624-631
50. Malmodin D, Papavoine CH, Billeter M (2003) Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR 27:69-79
51. Masse JE, Keller R (2005) AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic. J Magn Reson 174:133-151
52. Masse JE, Keller R, Pervushin K (2006) SideLink: Automated side-chain assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic. J Magn Reson 181:45-67
53. Meadows RP, Olejniczak ET, Fesik SW (1994) A computer-based protocol for semiautomated assignments and 3D structure determination of proteins. J Biomol NMR 4:79-96
54. 15N triple resonance experiments. J Magn Reson 87:183-188
55. Morelle N, Brutscher B, Simorre JP, Marion D (1995) Computer assignment of the backbone resonances of labelled proteins using two-dimensional correlation experiments. J Biomol NMR 5:154-160
56. 13 C chemical shifts. J Biomol NMR 29:1-9
57. Moseley H, Montelione G (1999) Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol 9:635-642
58. Moseley H, Monleon D, Montelione G (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 339:91-108
59. Mumenthaler C, Braun W (1995) Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J Mol Biol 254:465-480
60. Mumenthaler C, Güntert P, Braun W, Wüthrich K (1997) Automated combined assignment of NOESY and three-dimensional protein structure determination. J Biomol NMR 10:351-362
61. Neidig KP, Geyer M, Görler A, Antz C, Saffrich R, Beneicke W, Kalbitzer HR (1995) AURELIA, a program for computer-aided analysis of multidimensional NMR spectra. J Biomol NMR 6:255-270
62. Oezguen N, Adamian L, Xu Y, Rajarathnam K, Braun W (2002) Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra. J Biomol NMR 22:249-263
63. Olson JB, Markley JL (1994) Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: A demonstration of the connectivity tracing assignment tools (CONTRAST) software package. J Biomol NMR 4:385-410
64. Orekhov VY, Ibraghimov V, Billeter M (2001) MUNIN: A new approach to multi-dimensional NMR spectra interpretation. J Biomol NMR 20:49-60
65. Oschkinat H, Croft D (1994) Automated assignment of multidimensional nuclear magnetic resonance spectra. Methods Enzymol 239:308-318
66. Oschkinat H, Holak T, Cieslar C (1991) Assignment of protein NMR spectra in the light of homonuclear 3D spectroscopy: An automatable procedure based on 3D TOCSY-TOCSY and 3D TOCSY-NOESY. Biopolymers 31:699-712
67. Ou HD, Lai HC, Serber Z, Dötsch V (2001) Efficient indentification of amino acid types for fast protein backbone assignments. J Biomol NMR 21:269-273
68. Pons J, Delsuc M (1999) RESCUE: An artificial neural network tool for the NMR spectral assignment of proteins. J Biomol NMR 15:15-26
69. Pristovšek P, Rüterjans H, Jerala R (2002) Semiautomatic sequence-specific assignment of proteins based on the tertiary structure-the program st2nmr. J Comput Chem 23:335-340
70. 15N correlations. J Magn Reson 141:34-43
71. 15N correlations, III. J Magn Reson 153:186-192
72. 15N correlations, II. J Magn Reson 148:61-72
73. Slupsky CM, Boyko RF, Booth VK, Sykes BD (2003) Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments. J Biomol NMR 27:313-321
74. 13C-labeled proteins with projected 4D triple resonance NMR experiments. J Biomol NMR 11:387-405
75. Szyperski T, Yeh DC, Sukumaran DK, Moseley HN, Montelione GT (2002) Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc Natl Acad Sci USA 99:8009-8014
76. Tian F, Valafar H, Prestegard J (2001) A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. J Am Chem Soc 123:11791-11796
77. van de Ven FJ (1990) PROSPECT, a program for automated interpretation of 2D NMR spectra of proteins. J Magn Reson 86:633-644
78. Vitek O, Bailey-Kellogg C, Craig B, Kuliniewicz P, Vitek J (2005) Reconsidering complete search algorithms for protein backbone NMR assignment. Bioinformatics 21:230-236
79. Vitek O, Bailey-Kellogg C, Craig B, Vitek J (2006) Interential backbone assignment for sparse data. J Biomol NMR 35:187-208
80. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinás M, Ulrich EL, Markley JL, Ionides J, Laue ED (2005) The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins 59:687-696
81. Wan X, Lin G (2006) A graph-based automated NMR backbone resonance sequential assignment. In: Computational systems bioinformatics 2006 conference proceedings, vol 4, pp 55-66
82. Wan X, Xu D, Slupsky CM, Lin G (2003) Automated protein NMR resonance assignments. In: Proceedings of the IEEE computer society conference on bioinformatics, vol 2, pp 197-208
83. Wang J, Wang T, Zuiderweg ER, Crippen GM (2005) CASA: An efficient automated assignment of protein mainchain NMR data using an ordered tree search algorithm. J Biomol NMR 33:261-279
84. Wehrens R, Buydens L, Kateman G (1991) Validation and refinement of expert systems - interpretation of NMR-spectra as an application in analytical-chemistry. Chemometr Intell Lab Syst 12:57-67
85. Wehrens R, Lucasius C, Buydens L, Kateman G (1993a) HIPS, a hybrid self-adapting expert system for nuclear magnetic resonance spectrum interpretation using genetic algorithms. Anal Chim Acta 277:313-324
86. Wehrens R, Lucasius C, Buydens L, Kateman G (1993b) Sequential assignment of 2D-NMR spectra of proteins using genetic algorithms. J Chem Inf Comput Sci 33:245-251
87. 15N random coil NMR chemical shifts of the common amino acids. I. Investigation of nearest-neighbour effects. J Biomol NMR 5:67-81
88. Wu KP, Chang JM, Chen JB, Chang CF, Wu WJ, Huang TH, Sung TY, Hsu WL (2006) RIBRA - an error-tolerant algorithm for the NMR backbone assignment problem. J Comput Biol 13:229-244
89. 1H resonances from MQF-COSY. J Chem Inf Comput Sci 33:490-500
90. Xu J, Strauss S, Sanctuary B, Trimble L (1994) Use of fuzzy mathematics for complete automated assignment of peptide 1H 2D NMR spectra. J Magn Reson B103:53-58
91. Xu Y, Xu D, Kim D, Olman V, Razumovskaya J, Jiang T (2002) Automated assignment of backbone NMR peaks using constrained bipartite matching. Comput Sci Eng 4:50-62
92. Xu Y, Wang X, Yang J, Vaynberg J, Qin J (2006) PASA - a program for automated protein NMR backbone signal assignment by pattern-filtering approach. J Biomol NMR 34:41-56
93. Zimmerman DE, Montelione GT (1995) Automated analysis of nuclear magnetic resonance assignments for proteins. Curr Opin Struct Biol 5:664-673
94. Zimmerman D, Kulikowski C, Wang L, Lyons B, Montelione GT (1994) Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence. J Biomol NMR 4:241-256
95. Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien Cy, Montelione GT (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592-610