Abstract
The identification of sequence-based protein domains and their boundaries is often a prelude to structure determination. An accurate prediction of disordered regions, secondary structures and low complexity segments of target protein sequences can improve the efficiency of selection in structural genomics and also aid in design of constructs for directed structural biology studies. At the Center for Eukaryotic Structural Genomics (CESG) we have developed DomainView, a web tool to visualize and analyze predicted protein domains, disordered regions, secondary structures and low complexity segments of target protein sequences for selection of experimental protein structure attempts. DomainView consists of a relational database and a web graphical-user interface. The database was developed based on MySQL, which stores data from target protein sequences and their domains, disordered regions, secondary structures and low complexity segments. The program of the web user interface is a Perl CGI script. When a user searches for a target protein sequence, the script displays the combinational information about the domains and other features of that target sequence graphically on a web page by querying the database. The graphical representation for each feature is linked to a web page showing more detailed annotation information or to a new window directly running the corresponding prediction program to show further information about that feature.
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References
Brenner SE (2000) Target selection for structural genomics. Nat Struct Biol 7(Suppl):967–969
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL et al (2004) The Pfam protein family database. Nucleic Acid Res 32:138–141
Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH (2003) CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 31:383–387
Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2:953–971
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring mathrics. J Mol Biol 292:195–202
Garner E, Cannon P, Romero P, Obradovic Z, Dunker AK (1998) Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Inform 9:201–214
Tusnády GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17(9):849–850
Wootton JC, Federhen S (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput Chem 17:149–163
Acknowledgments
We thank CESG IT core staff and other staff who supported this development work by providing computer services and making suggestions. This project is supported by NIH/NIGMS Grant U54 GM074901.
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Pan, X., Bingman, C.A., Wesenberg, G.E. et al. Domain view: a web tool for protein domain visualization and analysis. J Struct Funct Genomics 11, 241–245 (2010). https://doi.org/10.1007/s10969-010-9097-4
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DOI: https://doi.org/10.1007/s10969-010-9097-4