Abstract
The Energy Distribution Markup Language (EDML) is an XML-based format that we have designed and developed to exchange protein structure energy profiles between many computers and users. Energy profiles that are distributions of various potential energies over consecutive atoms in protein molecular structures can be downloaded from the Energy Distribution Data Bank (EDB, http://edb.aei.polsl.pl) in the EDML format. In the paper, we describe the purpose of the EDML, a possible use of energy profiles, and internal structure of documents created in the EDML format.
Scientific research supported by the Ministry of Science and Higher Education, Poland in years 2008-2010, Grant No. N N516 265835: Protein Structure Similarity Searching in Distributed Multi Agent System.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Mrozek, D., Małysiak-Mrozek, B., et al.: The Energy Distribution Data Bank: Collecting energy features of protein molecular structures. In: IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2009, Taiwan, pp. 1–6 (2009)
Leach, A.: Molecular Modelling: Principles and Applications, 2nd edn. Pearson Education EMA, UK (2001)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)
Mrozek, D., et al.: Searching for Strong Structural Protein Similarities with EAST. Journal of Computer Assisted Mechanics and Engineering Sciences 14, 681–693 (2007)
Znamirowski, A.W., Znamirowski, L.: Two-Phase Simulation of Nascent Protein Folding. In: Proc. of the 4th IASTED Inter. Conference on Modelling, Simulation, and Optimization 2004, Kauai, Hawaii, pp. 293–298. ACTA Press (2004)
Mrozek, D., Małysiak, B., Kozielski, S.: Energy Profiles in Detection of Protein Structure Modifications. In: IEEE International Conference on Computing and Informatics, Kuala Lumpur, pp. 1–6 (2006)
Branden, C., Tooze, J.: Introduction to Protein Structure. Garland (1991)
Allen, J.P.: Biophysical Chemistry. Wiley-Blackwell (2008)
Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., et al.: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32(Database issue), D115–D119 (2004)
Wu, C.H., Yeh, L.S.L., Huang, H., Arminski, L., et al.: The Protein Information Resource. Nucleic Acids Research 31, 345–347 (2003)
Peptide/Protein Sequence Database (PRF/SEQDB), The Protein Research Foundation, http://www4.prf.or.jp/en/pn.html
Wheeler, D.L., Chappey, C., Lash, A.E., Leipe, D.D., et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 28(1), 10–14 (2000)
Lodish, H., Berk, A., Zipursky, S.L., et al.: Molecular Cell Biology, 4th edn. W. H. Freeman and Company, New York (2001)
Creighton, T.E.: Proteins: Structures and molecular properties, 2nd edn. Freeman, San Francisco (1993)
Boutselakis, H., Copeland, J., et al.: E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res. 31, 458–462 (2003)
Marchler-Bauer, A., Addess, K.J., Chappey, C., et al.: MMDB: Entrez’s 3D structure database. Nucleic Acids Res. 27(1), 240–243 (1999)
Bourne, P.E., Berman, H.M., Watenpaugh, K., et al.: The macromolecular Crystallographic Information File (mmCIF). Methods Enzymol. 277, 571–590 (1997)
Ohkawa, H., Ostell, J., Bryant, S.: MMDB: an ASN.1 specification for macromolecular structure. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 259–267 (1995)
Wesbrook, J., Ito, N., Nakamura, H., et al.: PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21(7), 988–992 (2005)
Cornell, W.D., et al.: A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 117, 5179–5197 (1995)
Bray, T., Paoli, J., et al.: Extensible Markup Language (XML) 1.0 (5th edn.). W3C Recommendation (November 26, 2008), http://www.w3.org/XML (visited 2009)
Ponder, J.W., Case, D.A.: Force Fields for Protein Simulation. Adv. Prot. Chem. 66, 27–85 (2003)
Berglund, A., Boag, S., Chamberlin, D., et al.: XML Path Language (XPath) 2.0. W3C Recommendation (January 23, 2007), http://www.w3.org/TR/xpath20/ (visited 2009)
Boag, S., Chamberlin, D., Fernández, M.F., et al.: XQuery 1.0: An XML Query Language. W3C Recommendation (January 23, 2007), http://www.w3.org/TR/xquery/ (visited 2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Mrozek, D., Małysiak-Mrozek, B., Kozielski, S., Górczyńska-Kosiorz, S. (2009). The EDML Format to Exchange Energy Profiles of Protein Molecular Structures. In: Huang, DS., Jo, KH., Lee, HH., Kang, HJ., Bevilacqua, V. (eds) Emerging Intelligent Computing Technology and Applications. ICIC 2009. Lecture Notes in Computer Science, vol 5754. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04070-2_17
Download citation
DOI: https://doi.org/10.1007/978-3-642-04070-2_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04069-6
Online ISBN: 978-3-642-04070-2
eBook Packages: Computer ScienceComputer Science (R0)