Practical application of bioinformatics by the multidisciplinary VIZIER consortium

Antiviral Research

Volumn 87, Issue 2, 2010, Pages 95-110

  Gorbalenya, Alexander E ^a,b   Lieutaud, Philippe ^c   Harris, Mark R ^d   Coutard, Bruno ^c   Canard, Bruno ^c   Kleywegt, Gerard J ^d   Kravchenko, Alexander A ^b   Samborskiy, Dmitry V ^a   Sidorov, Igor A ^a   Leontovich, Andrey M ^b   Jones, T Alwyn ^d  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

^c Centre National de la Recherche Scientifique   (France)

^d UPPSALA UNIVERSITY   (Sweden)

Author keywords

EDBase; VaZyMolO; VirAliS; VIZIER; Xtrack

Indexed keywords

ANTIVIRUS AGENT; ENZYME; VIRUS PROTEIN;

BIOINFORMATICS; BIOTECHNOLOGY; COMPUTER PROGRAM; DATA BASE; DOMESTIC ANIMAL; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; INFECTION; INFLUENZA VIRUS; LIBRARY SCIENCE; NONHUMAN; PATHOGENESIS; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN TARGETING; REVIEW; RNA VIRUS; VIRUS IDENTIFICATION; ANIMAL; BIOLOGY; CHEMISTRY; DRUG EFFECTS; ENZYMOLOGY; EUROPEAN UNION; GENETICS; HUMAN; MEDICAL RESEARCH; METABOLISM; ORGANIZATION AND MANAGEMENT; PROCEDURES; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; TRENDS; VIRUS REPLICATION;

ANIMALS; BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENZYMES; EUROPEAN UNION; HUMANS; PROTEIN STRUCTURE, TERTIARY; RNA VIRUSES; VIRAL PROTEINS; VIRUS REPLICATION;

ANIMALIA; HEPATITIS C VIRUS; ORTHOMYXOVIRIDAE; RNA VIRUSES;

EID: 77954913577     PISSN: 01663542     EISSN: 18729096     Source Type: Journal    
DOI: 10.1016/j.antiviral.2010.02.005     Document Type: Review

References (89)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389-3402.
2. Bairoch A., UniProt Consortium, Bougueleret L., Altairac S., Amendolia V., Auchincloss A., Argoud-Puy G., Axelsen K., Baratin D., Blatter M.C., Boeckmann B., Bolleman J., Bollondi L., Boutet E., Quintaje S.B., Breuza L., Bridge A., Decastro E., Ciapina L., Coral D., Coudert E., Cusin I., Delbard G., Dornevil D., Roggli P.D., Duvaud S., Estreicher A., Famiglietti L., Feuermann M., Gehant S., Farriol-Mathis N., Ferro S., Gasteiger E., Gateau A., Gerritsen V., Gos A., Gruaz-Gumowski N., Hinz U., Hulo C., Hulo N., James J., Jimenez S., Jungo F., Junker V., Kappler T., Keller G., Lachaize C., Lane-Guermonprez L., Langendijk-Genevaux P., Lara V., Lemercier P., Le Saux V., Lieberherr D., Lima T.D., Mangold V., Martin X., Masson P., Michoud K., Moinat M., Morgat A., Mottaz A., Paesano S., Pedruzzi I., Phan I., Pilbout S., Pillet V., Poux S., Pozzato M., Redaschi N., Reynaud S., Rivoire C., Roechert B., Schneider M., Sigrist C., Sonesson K., Staehli S., Stutz A., Sundaram S., Tognolli M., Verbregue L., Veuthey A.L., Yip L., Zuletta L., Apweiler R., Alam-Faruque Y., Antunes R., Barrell D., Binns D., Bower L., Browne P., Chan W.M., Dimmer E., Eberhardt R., Fedotov A., Foulger R., Garavelli J., Golin R., Horne A., Huntley R., Jacobsen J., Kleen M., Kersey P., Laiho K., Leinonen R., Legge D., Lin Q., Magrane M., Martin M.J., O'Donovan C., Orchard S., O'Rourke J., Patient S., Pruess M., Sitnov A., Stanley E., Corbett M., di Martino G., Donnelly M., Luo J., van Rensburg P., Wu C., Arighi C., Arminski L., Barker W., Chen Y.X., Hu Z.Z., Hua H.K., Huang H.Z., Mazumder R., McGarvey P., Natale D.A., Nikolskaya A., Petrova N., Suzek B.E., Vasudevan S., Vinayaka C.R., Yeh L.S., Zhang J. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Research 2009, 37:D169-D174.
3. Belshaw R., de Oliveira T., Markowitz S., Rambaut A. The RNA virus database. Nucleic Acids Research 2009, 37:D431-D435.
4. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Research 2008, 36:D25-D30.
5. Berman H., Henrick K., Nakamura H., Markley J.L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research 2007, 35:D301-D303.
6. Blanc E., Roversi P., Vonrhein C., Flensburg C., Lea S.M., Bricogne G. Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Cryst. 2004, D60:2210-2221.
7. Blom N., Hansen J., Blaas D., Brunak S. Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks. Protein Science 1996, 5:2203-2216.
8. Bryson K., Cozzetto D., Jones D.T. Computer-assisted protein domain boundary prediction using the Dom-Pred server. Current Protein & Peptide Science 2007, 8:181-188.
9. Carugo O., Djinovic-Carugo K., Gorbalenya A.E., Tucker P. Workshop on the definition of protein domains and their likelihood of crystallization - editorial. Current Protein & Peptide Science 2007, 8:119-120.
10. Chen J., Swamidass S.J., Bruand J., Baldi P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics 2005, 21:4133-4139.
11. Collaborative Computational Project, N.4 The CCP4 suite: programs for protein crystallography. Acta Crystallographica 1994, D50:760-763.
12. Coutard B., Gorbalenya A.E., Snijder E.J., Leontovich A.M., Poupon A., de Lamballerie X., Charrel R., Gould E.A., Gunther S., Norder H., Klempa B., Bourhy H., Rohayem J., L'hermite E., Nordlund P., Stuart D.I., Owens R.J., Grimes J.M., Tucker P.A., Bolognesi M., Mattevi A., Coll M., Jones T.A., Aqvist J., Unge T., Hilgenfeld R., Bricogne G., Neyts J., La Colla P., Puerstinger G., Gonzalez J.P., Leroy E., Cambillau C., Romette J.L., Canard B. The VIZIER project: preparedness against pathogenic RNA viruses. Antiviral Research 2008, 78:37-46.
13. Crowder S., Kirkegaard K. Trans-dominant inhibition of RNA viral replication can slow growth of drug-resistant viruses. Nature Genetics 2005, 37:701-709.
14. Delaney J.S. Finding and filling protein cavities using cellular logic operations. J. Mol. Graphics 1992, 10:174.
15. Dovidchenko N.V., Lobanov M.Y., Galzitskaya O.V. Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone. Current Protein & Peptide Science 2007, 8:189-195.
16. Dumontier M., Yao R., Feldman H.J., Hogue C.W.V. Armadillo: domain boundary prediction by amino acid composition. Journal of Molecular Biology 2005, 350:1061-1073.
17. Eddy S.R. Hidden Markov models. Current Opinion in Structural Biology 1996, 6:361-365.
18. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
19. Feder M., Pas J., Wyrwicz L.S., Bujnicki J.M. Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. Gene 2003, 302:129-138.
20. Ferron F., Longhi S., Henrissat B., Canard B. Viral RNA-polymerases - a predicted 2'-O-ribose methyltransferase domain shared by all Mononegavirales. Trends in Biochemical Sciences 2002, 27:222-224.
21. Ferron F., Rancurel C., Longhi S., Cambillau C., Henrissat B., Canard B. VaZyMolO: a tool to define and classify modularity in viral proteins. Journal of General Virology 2005, 86:743-749.
22. Finn R.D., Tate J., Mistry J., Coggill P.C., Sammut S.J., Hotz H.R., Ceric G., Forslund K., Eddy S.R., Sonnhammer E.L., Bateman A. The Pfam protein families database. Nucleic Acids Research 2008, 36:D281-D288.
23. Galzitskaya O.V., Garbuzynskiy S.O., Lobanov M.Y. FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics 2006, 22:2948-2949.
24. George R.A., Heringa J. SnapDRAGON: a method to delineate protein structural domains from sequence data. Journal of Molecular Biology 2002, 316:839-851.
25. Gohara D.W., Ha C.S., Kumar S., Ghosh B., Arnold J.J., Wisniewski T.J., Cameron C.E. Production of " authentic" poliovirus RNA-dependent RNA polymerase (3D(pol)) by ubiquitin-protease-mediated cleavage in Escherichia coli. Protein Expression and Purification 1999, 17:128-138.
26. Golovin A., Oldfield T.J., Tate J.G., Velankar S., Barton G.J., Boutselakis H., Dimitropoulos D., Fillon J., Hussain A., Ionides J.M.C., John M., Keller P.A., Krissinel E., McNeil P., Naim A., Newman R., Pajon A., Pineda J., Rachedi A., Copeland J., Sitnov A., Sobhany S., Suarez-Uruena A., Swaminathan G.J., Tagari M., Tromm S., Vranken W., Henrick K. E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Research 2004, 32(Database issue):D211-D216.
27. Gorbalenya A.E. Host-related sequences in RNA virus genomes. Seminars in Virology 1992, 3:359-371.
28. Gorbalenya A.E. Origin of RNA viral genomes; approaching the problem by comparative sequence analysis. Molecular Basis of Virus Evolution 1995, 49-66. Cambridge University Press, Cambridge, UK. A.J. Gibbs, C.H. Calisher, F. Garcia-Arenal (Eds.).
29. Gorbalenya A.E. Big nidovirus genome - when count and order of domains matter. Advances in Experimental Medicine and Biology 2001, 494:1-17.
30. Gorbalenya A.E., Donchenko A.P., Blinov V.M., Koonin E.V. Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases: a distinct protein superfamily with a common structural fold. FEBS Letters 1989, 243:103-114.
31. Gorbalenya A.E., Donchenko A.P., Koonin E.V., Blinov V.M. N-Terminal domains of putative helicases of flavi- and pestiviruses may be serine proteases. Nucleic Acids Research 1989, 17:3889-3897.
32. Gorbalenya A.E., Enjuanes L., Ziebuhr J., Snijder E.J. Nidovirales: evolving the largest RNA virus genome. Virus Research 2006, 117:17-37.
33. Gorbalenya A.E., Koonin E.V. Comparative analysis of the amino acid sequences of the key enzymes of the replication and expression of positive-strand RNA viruses. Validity of the approach and functional and evolutionary implications. Soviet Science Reviews D: Physicochemical Biology 1993, 11:1-84.
34. Gorbalenya A.E., Koonin E.V. Helicases: amino acid sequence comparisons and structure-function relationships. Current Opinion in Structural Biology 1993, 3:419-429.
35. Gorbalenya A.E., Koonin E.V., Donchenko A.P., Blinov V.M. Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis. Nucleic Acids Research 1989, 17:4847-4861.
36. Gorbalenya A.E., Koonin E.V., Lai M.M.C. Putative papain-related thiol proteases of positive-strand RNA viruses. FEBS Letters 1991, 288:201-205.
37. Gorbalenya A.E., Snijder E.J. Viral cysteine proteinases. Perspectives in Drug Discovery and Design 1996, 6:64-86.
38. Gromeier M., Wimmer E., Gorbalenya A.E. Genetics, pathogenesis and evolution of picornaviruses. Origin and Evolution of Viruses 1999, 287-343. Academic Press, San Diego. E. Domingo, R.G. Webster, J.J. Holland (Eds.).
39. Hansen J.L., Long A.M., Schultz S.C. Structure of the RNA-dependent RNA polymerase of poliovirus. Structure (Cambridge) 1997, 5:1109-1122.
40. Harris M., Jones T.A. Xtrack - a web-based crystallographic notebook. Acta Crystallographica D: Biological Crystallography 2002, 58:1889-1891.
41. Hartshorn M.J. AstexViewer: a visualisation aid for structure-based drug design. Journal of Computer-Aided Molecular Design 2002, 16:871-881.
42. Hendlich M., Bergner A., Gunther J., Klebe G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. Journal of Molecular Biology 2003, 326:607-620.
43. Hughes P.J., Stanway G. The 2A proteins of three diverse picornaviruses are related to each other and to the H-rev107 family of proteins involved in the control of cell proliferation. Journal of General Virology 2000, 81:201-207.
44. Hulo N., Bairoch A., Bulliard V., Cerutti L., Cuche B.A., de Castro E., Lachaize C., Langendijk-Genevaux P.S., Sigrist C.J. The 20 years of PROSITE. Nucleic Acids Research 2008, 36:D245-D249.
45. Jansson A.M., Jakobsson E., Johansson P., Lantez V., Coutard B., de Lamballerie X., Unge T., Jones T.A. Structure of the methyltransferase domain from the Modoc virus, a flavivirus with no known vector. Acta Crystallographica 2009, D65:1-10.
46. Jiang P., Faase J.A.J., Toyoda H., Paul A., Wimmer E., Gorbalenya A.E. Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:9457-9462.
47. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. 1991, A47:110-119.
48. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
49. Kamer G., Argos P. Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial-viruses. Nucleic Acids Research 1984, 12:7269-7282.
50. Kiemer L., Lund O., Brunak S., Blom N. Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology. BMC Bioinformatics 2004, 5:72.
51. Kitamura N., Semler B.L., Rothberg P.G., Larsen G.R., Adler C.J., Dorner A.J., Emini E.A., Hanecak R., Lee J.J., Vanderwerf S., Anderson C.W., Wimmer E. Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature 1981, 291:547-553.
52. Kleywegt G.J., Harris M.R. ValLigURL: a server for ligand-structure comparison and validation. Acta Crystallographica D 2007, 63:935-938.
53. Kleywegt G.J., Harris M.R., Zou J.Y., Taylor T.C., Wahlby A., Jones T.A. The Uppsala electron-density server. Acta Crystallographica D: Biological Crystallography 2004, 60:2240-2249.
54. Kleywegt G.J., Jones T.A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallographica 1994, D50:178-185.
55. Kleywegt G.J., Jones T.A. Where freedom is given, liberties are taken. Structure 1995, 3:535-540.
56. Kleywegt G.J., Jones T.A. Efficient rebuilding of protein structures. Acta Crystallographica 1996, D52:829-832.
57. Kleywegt G.J., Jones T.A. Phi/Psi-chology: Ramachandran revisited. Structure 1996, 4:1395-1400.
58. Kleywegt G.J., Jones T.A. Detecting folding motifs and similarities in protein structures. Methods in Enzymology 1997, 277:525-545.
59. Kleywegt G.J., Jones T.A. Model-building and refinement practice. Methods in Enzymology 1997, 277:208-230.
60. Koonin E.V Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and λ2 protein of reovirus. Journal of General Virology 1993, 74:733-740.
61. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology 2001, 305:567-580.
62. Leontovich A.M., Tokmachev K.Y., van Houwelingen H.C. The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem. BMC Bioinformatics 2008, 9:31.
63. Lieutaud P., Canard B., Longhi S. MeDor: a metaserver for predicting protein disorder. BMC Genomics 2008, 9(Suppl. 2):S25.
64. Liu T., Lin Y., et al. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research 2007, 35(Database issue):D198-201.
65. Liu J.F., Rost B. Sequence-based prediction of protein domains. Nucleic Acids Research 2004, 32:3522-3530.
66. Marchler-Bauer A., Anderson J.B., Chitsaz F., Derbyshire M.K., DeWeese-Scott C., Fong J.H., Geer L.Y., Geer R.C., Gonzales N.R., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Lu S., Marchler G.H., Mullokandov M., Song J.S., Tasneem A., Thanki N., Yamashita R.A., Zhang D., Zhang N., Bryant S.H. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Research 2009, 37:D205-D210.
67. Mazumder R., Iyer L.M., Vasudevan S., Aravind L. Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Nucleic Acids Research 2002, 30:5229-5243.
68. Michalsky E., Dunkel M., Goede A., Preissner R. SuperLigands - a database of ligand structures derived from the Protein Data Bank. BMC Bioinformatics 2005, 6:122.
69. Morgenstern B. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Research 2004, 32:W33-W36.
70. Moya A., Holmes E.C., Gonzalez-Candelas F. The population genetics and evolutionary epidemiology of RNA viruses. Nature Reviews Microbiology 2004, 2:279-288.
71. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica 1997, D53:240-255.
72. Neuman B.W., Joseph J.S., Saikatendu K.S., Serrano P., Chatterjee A., Johnson M.A., Liao L., Klaus J.P., Yates J.R., Wuethrich K., Stevens R.C., Buchmeier M.J., Kuhn P. Proteornics analysis unravels the functional repertoire of coronavirus nonstructural protein 3. Journal of Virology 2008, 82:5279-5294.
73. Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 2000, 302:205-217.
74. Paul A.V., van Boom J.H., Filippov D., Wimmer E. Protein-primed RNA synthesis by purified poliovirus RNA polymerase. Nature 1998, 393:280-284.
75. Ratia K., Saikatendu K.S., Santarsiero B.D., Barretto N., Baker S.C., Stevens R.C., Mesecar A.D. Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:5717-5722.
76. Rawlings N.D., Morton F.R., Kok C.Y., Kong J., Barrett A.J. MEROPS: the peptidase database. Nucleic Acids Research 2008, 36:D320-D325.
77. Rozanov M.N., Koonin E.V., Gorbalenya A.E. Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses. Journal of General Virology 1992, 73:2129-2134.
78. Sadreyev R., Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. Journal of Molecular Biology 2003, 326:317-336.
79. Serrano P., Johnson M.A., Almeida M.S., Horst R., Herrmann T., Joseph J.S., Neuman B.W., Subramanian V., Saikatendu K.S., Buchmeier M.J., Stevens R.C., Kuhn P., Wuthrich K. Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus. Journal of Virology 2007, 81:12049-12060.
80. Sidorov I.A., Reshetov D.A., Gorbalenya A.E. SNAD: sequence name annotation-based designer. BMC Bioinformatics 2009, 10:251.
81. Sim J., Kim S.Y., Lee J. PPRODO: prediction of protein domain boundaries using neural networks. Proteins-Structure Function and Bioinformatics 2005, 59:627-632.
82. Simossis V.A., Kleinjung J., Heringa J. Homology-extended sequence alignment. Nucleic Acids Research 2005, 33:816-824.
83. Snijder E.J., Bredenbeek P.J., Dobbe J.C., Thiel V., Ziebuhr J., Poon L.L.M., Guan Y., Rozanov M., Spaan W.J.M., Gorbalenya A.E. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. Journal of Molecular Biology 2003, 331:991-1004.
84. Suyama M, Ohara O. DomCut: prediction of inter-domain linker regions in amino acid sequences. Bioinformatics 2003, 19:673-674.
85. Thompson A.A., Peersen O.B. Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. EMBO Journal 2004, 23:3462-3471.
86. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997, 25:4876-4882.
87. Yang Z.R., Thomson R., McNeil P., Esnouf R.M. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 2005, 21:3369-3376.
88. Yoo P.D., Sikder A.R., Zhou B.B., Zomaya A.Y. Improved general regression network for protein domain boundary prediction. BMC Bioinformatics 2008, 9:S12.
89. Ziebuhr J., Thiel V., Gorbalenya A.E. The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond. Journal of Biological Chemistry 2001, 276:33220-33232.