Abstract
Proteins are macromolecules that facilitate virtually every biological process. Information on functional and structural characteristics of proteins is invaluable in life sciences, but remain difficult to obtain, both computationally and experimentally.
In recent work, we have introduced a novel method for functional characterization, which we refer to as protein energy profiling. The eProS (energy profile suite) is an online knowledgebase, toolbox and database that provides a webspace for protein energy profile analyses to the scientific community. The objective of eProS is to offer a free-for-all repository of energy profile data, annotations, visualizations, as well as tools that can aid in deducing relations complementing and supporting findings made by traditional bioinformatics methods.
In this paper, we discuss the underlying biological and theoretical backgrounds used by implemented methods and tools, and also introduce recent enhancements and developments.
eProS is available at http://bioservices.hs-mittweida.de/Epros.
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References
Andreeva, A., et al.: Data growth and its impact on the scop database: new developments. Nucleic Acids Res. 36(Database issue), D419–D425 (2008), http://dx.doi.org/10.1093/nar/gkm993
Blake, J.A., et al.: Gene ontology annotations and resources. Nucleic Acids Res. 41(Database issue), D530–D535 (2013), http://dx.doi.org/10.1093/nar/gks1050
Cuff, A.L., Sillitoe, I., Lewis, T., Clegg, A.B., Rentzsch, R., Furnham, N., Pellegrini-Calace, M., Jones, D., Thornton, J., Orengo, C.A.: Extending cath: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res. 39(Database issue), D420–D426 (2011), http://dx.doi.org/10.1093/nar/gkq1001
Dressel, F., Marsico, A., Tuukkanen, A., Schroeder, M., Labudde, D.: Understanding of SMFS barriers by means of energy profiles. In: Proceedings of German Conference on Bioinformatics, pp. 90–99 (2007)
Finn, R.D., et al.: Pfam: the protein families database. Nucleic Acids Res. 42(Database issue), D222–D230 (2014), http://dx.doi.org/10.1093/nar/gkt1223
Garnier, J., Gibrat, J.F., Robson, B.: Gor method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266, 540–553 (1996)
Heinke, F., Labudde, D.: Membrane protein stability analyses by means of protein energy profiles in case of nephrogenic diabetes insipidus. Comput. Math. Methods Med. 2012, 790281 (2012), http://dx.doi.org/10.1155/2012/790281
Heinke, F., Labudde, D.: Functional Analyses of Membrane Protein Mutants involved in Nephrogenic Diabetes insipidus: An Energy-based Approach. In: Research on Diabetes, 1st edn. iConcept Press Ltd. (2013)
Heinke, F., Schildbach, S., Stockmann, D., Labudde, D.: epros–a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. Nucleic Acids Res. 41(Database issue), D320–D326 (2013), http://dx.doi.org/10.1093/nar/gks1079
Mrozek, D., Malysiak, B., Kozielski, S.: An optimal alignment of proteins energy characteristics with crisp and fuzzy similarity awards. In: FUZZ-IEEE 2007, pp. 1–6 (2007)
Mrozek, D., Malysiak-Mrozek, B., Kozielski, S.: Alignment of protein structure energy patterns represented as sequences of fuzzy numbers. In: Annual Meeting of the North American Fuzzy Information Processing Society, NAFIPS 2009 (2009)
Prlić, A., et al.: Biojava: an open-source framework for bioinformatics in 2012. Bioinformatics 28(20), 2693–2695 (2012), http://dx.doi.org/10.1093/bioinformatics/bts494
Rose, P.W., et al.: The rcsb protein data bank: new resources for research and education. Nucleic Acids Res. 41(Database issue), D475–D482 (2013), http://dx.doi.org/10.1093/nar/gks1200
Schomburg, I., et al.: Brenda in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in brenda. Nucleic Acids Res. 41(Database issue), D764–D772 (2013), http://dx.doi.org/10.1093/nar/gks1049
UniProt Consortium: Activities at the universal protein resource (uniprot). Nucleic Acids Res. 42(Database issue), D191–D198 (2014), http://dx.doi.org/10.1093/nar/gkt1140
Webber, W., Moffat, A., Zobel, J.: A similarity measure for indefinite rankings. ACM Transactions on Information Systems 28 (2010)
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Heinke, F., Stockmann, D., Schildbach, S., Langer, M., Labudde, D. (2015). eProS – A Bioinformatics Knowledgebase, Toolbox and Database for Characterizing Protein Function. In: Kozielski, S., Mrozek, D., Kasprowski, P., Małysiak-Mrozek, B., Kostrzewa, D. (eds) Beyond Databases, Architectures and Structures. BDAS 2015. Communications in Computer and Information Science, vol 521. Springer, Cham. https://doi.org/10.1007/978-3-319-18422-7_51
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DOI: https://doi.org/10.1007/978-3-319-18422-7_51
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