Practical application of bioinformatics by the multidisciplinary VIZIER consortium - PubMed (original) (raw)

Review

Practical application of bioinformatics by the multidisciplinary VIZIER consortium

Alexander E Gorbalenya et al. Antiviral Res. 2010 Aug.

Abstract

This review focuses on bioinformatics technologies employed by the EU-sponsored multidisciplinary VIZIER consortium (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 PROJECT: 2004-511960, active from 1 November 2004 to 30 April 2009), to achieve its goals. From the management of the information flow of the project, to bioinformatics-mediated selection of RNA viruses and prediction of protein targets, to the analysis of 3D protein structures and antiviral compounds, these technologies provided a communication framework and integrated solutions for steady and timely advancement of the project. RNA viruses form a large class of major pathogens that affect humans and domestic animals. Such RNA viruses as HIV, Influenza virus and Hepatitis C virus are of prime medical concern today, but the identities of viruses that will threaten human population tomorrow are far from certain. To contain outbreaks of common or newly emerging infections, prototype drugs against viruses representing the Virus Universe must be developed. This concept was championed by the VIZIER project which brought together experts in diverse fields to produce a concerted and sustained effort for identifying and validating targets for antivirus therapy in dozens of RNA virus lineages.

Copyright 2010 Elsevier B.V. All rights reserved.

PubMed Disclaimer

Figures

Fig. 1

Fig. 1

VIZIER targets data pathway. Information stored into the VIZIER Targets Database can be accessed through the three VIZIER Targets DB interfaces including: (A) Targets Data; (B) Targets Status; (C) Target Focus. Xtrack provides also three Interfaces for users that are (D)–(F). Both VIZIER and Xtrack databases are inter-linked. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 2

Fig. 2

Rooted phylogenetic analysis of C cluster Human Enteroviruses for the structural part of polyprotein. Figure was modified from Fig. 1 in (Jiang et al., 2007).

Fig. 3

Fig. 3

Separate domains and their combinations (targets) predicted for RNA viruses with Viralis.

Fig. 4

Fig. 4

The VaZyMolO Browser Focus Interface. It allows browsing from genomic information to a protein's module details.

Fig. 5

Fig. 5

The MeDor program's output for phosphoprotein P24 of the Borna disease virus (accession number

P26668

). The highlighted regions in red and blue, and the textual comments constitute annotations made by a user. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 6

Fig. 6

Viralis Web interface to handle user queries and access targets predicted in RNA viruses.

Fig. 7

Fig. 7

Viralis Domain Prediction Response module interface.

Fig. 8

Fig. 8

ID-to-name conversion in tree of alphaviruses by SNAD.

Fig. 9

Fig. 9

Xtrack/EDBase components and interactions.

Fig. 10

Fig. 10

Xtrack project listing, centred on target VZ93. Some fields are clipped to the right of the image.

Fig. 11

Fig. 11

Access to EDBase for VZ93 example. (a) Four models (with goodness-of-fit indicators) are stored in the database and (b) solvent B-factor distribution after refinement.

Fig. 12

Fig. 12

(a) Access to ValLigURL for the VZ95 example. (b) JMol superposition of SAM (s-adenosylmethionine) to PDB entry 1JG4.

Similar articles

Cited by

References

    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. - PMC - PubMed
    1. 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. - PMC - PubMed
    1. Belshaw R., de Oliveira T., Markowitz S., Rambaut A. The RNA virus database. Nucleic Acids Research. 2009;37:D431–D435. - PMC - PubMed
    1. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Research. 2008;36:D25–D30. - PMC - PubMed
    1. 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. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources