Protein Engineering, Vol. 13, No. 6, 395-396,
June 2000
© 2000 Oxford University Press
Communications |
Interactive construction of residue-based diagrams of proteins: the RbDe web service
Department of Physiology and Biophysics, Box 1218, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA
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Abstract |
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 Top Abstract IntroductionOrganization of the serviceImplementationReferences |
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We announce the Residue-based Diagram Editor (RbDe) web service that allows online construction of residue-based diagrams and the creation of stored diagram libraries. The service has been tuned for the construction of snake-like diagrams (for transmembrane proteins) but can be used to render any protein for which defined secondary structure data or hypotheses are available. RbDe is freely available through the Internet from our web site: http://transport.physbio.mssm.edu/rbde/RbDe.html. Licenses for intranet uses can be obtained upon request.
Keywords: membrane proteins/residue-based diagrams of proteins/web service
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Introduction |
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TopAbstractIntroductionOrganization of the serviceImplementationReferences |
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Residue-based diagrams are a special kind of representation of a protein where residues are laid out on a page with conventions that highlight the relations between a given sequence, secondary structure information and residue-level annotations. For transmembrane proteins, where the representation is used extensively as a simplified model because of the lack of better structural information, the term snake-like diagram has been coined, inspired by the layout of the sequence that spans the membrane several times.
The automation of the rendering of snake-like diagrams, for proteins whose topology was similar to that of G protein-coupled receptors (GPCRs), was first published with the description of the Viseur program (Campagne et al., 1995–97
,1999). This first automation was important to database curators in the GPCR field as it allowed them to build snake-like diagrams of GPCRs, designed to present a specific aspect of a system. The GPCRDB database (Horn et al., 1998) uses such snake-like diagrams, built with the Viseur program, in order to (i) provide easy access to mutation data, each sequence in the database being associated with a snake-like diagram that shows mutated residues in a given color, and (ii) visualize correlated mutation analysis results (Wells, 1990).
A new method (Campagne and Weinstein, 1999) was developed to extend the automation of the rendering of residue-based diagrams to other kinds of topologies and to provide more flexibility in the control of the output than was possible with the first algorithm. We present here the Residue-based Diagram Editor (RbDe) web service that provides the interface for end-users to construct diagrams interactively for a sequence of interest.
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Organization of the service |
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TopAbstractIntroductionOrganization of the serviceImplementationReferences |
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The service consists of the following parts :
Import facility. Allows the user to import a sequence into the service. SwissProt sequences are transparently obtained through the network and other sequences can be typed in as text in a short list of sequence formats (SwissProt, PIR, Fasta, PDB). The secondary structure and transmembrane limit annotations are read when available in the given format. Disulfide bridges are read from SwissProt files to be represented on the diagram.
Topology editor. Provides a way to enter or refine the secondary structure and transmembrane limits hypotheses. Secondary structure elements can be chosen between helices and strands.
Annotation editor. Manages annotations attached to a residue. The annotations consist of the choice of a color and/or URL. Individual residues and ranges can be linked to end-user documents that describe an aspect of the system to which they relate.
Diagram editor. Manages parameters that affect the rendering of the diagram as a whole. Currently, these parameters are direction of the N-terminal segment on the page, reduction factor to be applied to the diagram and coloring of the residues which are not annotated.
Diagram viewer. Presents the diagram as customized by the user and enables the links defined in the annotation editor.
Diagram library. Allows end-users to store the diagrams they created with the service. Stored diagrams can be retrieved to be completed (addition of annotations) or simply consulted. (The library currently enforces that only the creator of a diagram can consult and change it.)
Figure 1 presents the sequence of Connexin50 (SwissProt ID: CXA8HUMAN) where the location of the residue 87 (proline) is identified. Mutation to a serine at this locus causes a congenital cataract (Shiels et al., 1998).
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Implementation |
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TopAbstractIntroductionOrganization of the serviceImplementationReferences |
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RbDe has been implemented as two Java packages that make use of the Servlet Application Programming Interface (JavaSoft, 1999a
). The first package (edu.mssm.crover.scentral) regroups features (e.g. user authentication, repository of URLs, page templates, pool of database connections, basic support for persistence, etc.) that are likely to be shared among additional web services to be developed in the future. The second package (edu.mssm.crover.rbdeservice) contains the Servlets we use to construct the user interface. The implementation of edu.mssm.crover.domain2d, described recently (Campagne and Weinstein, 1999), is used to build the diagrams as directed by the parameters edited through rbdeservice. The diagram library is implemented via the JDBC Application Programming Interface (JavaSoft, 1999b) that provides access to a relational database. Conclusion
The RbDe web service can be used to build residue-based diagrams of proteins online. The service provides significant flexibility in the construction of the diagrams and their annotations. Experience with the use of mutation databases (e.g. TinyGRAP) indicates that RbDe should be attractive resource for experimentalists who need these kind of diagrams to summarize and communicate results as well as plan future experiments. The diagrams built with the service can be reused programmatically to present the result of computational analysis (for instance, to present the location of predicted-turns on the sequence, etc.). Documentation of the Application Programming Interface necessary for doing so is available on-line at http://transport.physbio.mssm.edu/joe.
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Notes |
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1 To whom correspondence should be addressed.
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Acknowledgments |
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This work was supported by National Institute of Health grant DA12408.
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References |
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TopAbstractIntroductionOrganization of the serviceImplementationReferences |
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Campagne,F., Bernassau,J.-M. and Maigret,B. (1995–97) The Viseur Program. Laboratoire de Chimie Theoretique de Nancy, Nancy. WWW: http://transport.physbio.mssm.edu/viseur/viseur.html. Viseur Project home page.
Campagne,F., Jestin,R., Reversat,J., Bernassau,J. and Maigret,B. (1999) J. Comput.-Aided Mol. Des., 13, 625–643.
Campagne,F. and Weinstein,H. (1999) J. Mol. Graph. Mod., 17, 207–213.[Web of Science][Medline]
Horn,F., Weare,J., Beukers,M., Horsch,S., Bairoch,A., Chen,W., Edvardsen,O., Campagne,F. and Vriend,G. (1998) Nucleic Acids Res., 1, 275–279; see also URL: http://www.gpcr.org/7tm.
JavaSoft. (1999a). Java Servlet API. URL: http://java.sun.com/products/servlet/, Dec.
JavaSoft. (1999b). JDBC API. URL: http://java.sun.com/products/jdbc/, Dec.
Kristiansen,K., Dahl,G.S. and Edvardsen,O. (1996) Proteins: Struct. Funct. Genet., 26, 81–94.[Web of Science][Medline]
Shiels,A., Mackay,D., Ionides,A., Berry,V., Moore,A. and Bhattacharya,S. (1998) Am. J. Hum. Genet., 62, 526–532.[Web of Science][Medline]
Wells,J. (1990). Biochemistry, 29, 8509–8517.[Medline]
Received January 28, 2000; revised March 15, 2000; accepted March 22, 2000.
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