Abstract
Molecular viewers allow visualization of spatial structures of proteins and other biological molecules. However, most of them are not able to read molecular structures stored in the PDBML format provided by the world-wide Protein Data Bank (PDB). In the paper, we present main features of the MViewer that we have designed and developed in order to support a man-protein structure interaction. The unique feature of the MViewer is the ability to open, read and visualize structures stored in all three formats (i.e. PDB, mmCIF, and PDBML) available from the PDB repository.
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
Burkowski, F.: Structural Bioinformatics: An Algorithmic Approach, 1st edn. Chapman and Hall/CRC (2008)
Malysiak, B., Mrozek, D., Kozielski, S., Znamirowski, L.: Signal transduction simulation in nanoprocesses using distributed database environment. In: Modelling, Simulation, and Optimization: Fifth IASTED International Conference Proceedings, pp. 17–22 (2005)
Branden, C., Tooze, J.: Introduction to Protein Structure, 2nd edn. Garland Science (1999)
Berman, H., et al.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)
Westbrook, J., Fitzgerald, P.: The PDB format, mmCIF, and other data formats. Methods Biochem. Anal. 44, 161–179 (2003)
Gasteiger, J., Engel, T.: Chemoinformatics: a textbook. Wiley-VCH (2003)
Bourne, P., Berman, H., Watenpaugh, K., et al.: The macromolecular crystallographic information file (mmCIF). Methods Enzymol. 277, 571–590 (1997)
Wesbrook, J., Ito, N., Nakamura, H., Henrick, K., Berman, H.: PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21(7), 988–992 (2005)
Sayle, R.: RasMol, Molecular Graphics Visualization Tool. Biomolecular Structures Group, Glaxo Welcome Research & Development, Stevenage, Hartfordshire (1998), http://www.umass.edu/microbio/rasmol/ (February 5, 2013)
Chime and Jmol Homepage: Molecular Visualization Resources, http://www.umass.edu/microbio/chime/
Jmol Homepage: Jmol: an open-source Java viewer for chemical structures in 3D, http://www.jmol.org
Gans, J., Shalloway, D.: Qmol: a program for molecular visualization on Windows-based PCs. J. Mol. Graph. Model. 19(6), 557–559 (2001)
The PyMOL molecular graphics system, ver. 1.3r1. Schrödinger, LLC (2010), http://www.pymol.org
Hogue, C.: Cn3D: a new generation of three-dimensional molecular structure viewer. Trends Biochem. Sci. 8, 314–316 (1997)
Mrozek, D., Mastej, A., Malysiak, B.: Protein Molecular Viewer for visualizing structures stored in the PDBML format. In: Pietka, E., Kawa, J. (eds.) Information Technologies in Biomedicine. AISC, vol. 47, pp. 377–386. Springer, Heidelberg (2008)
Bellazzi, R., Masseroli, M., Murphy, S., Shabo, A., Romano, P.: Clinical Bioinformatics: challenges and opportunities. BMC Bioinformatics 13(suppl. 14), S1 (2012)
Mrozek, D., Małysiak-Mrozek, B., Siaznik, A.: search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information. BMC Bioinformatics 14, 73 (2013)
Burczyński, T., Poteralski, A., Szczepanik, M.: Topological evolutionary computing in the optimal design of 2D and 3D structures. Engineering Optimization 39(7), 811–830 (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Stanek, D., Mrozek, D., Małysiak-Mrozek, B. (2013). MViewer: Visualization of Protein Molecular Structures Stored in the PDB, mmCIF and PDBML Data Formats. In: Kwiecień, A., Gaj, P., Stera, P. (eds) Computer Networks. CN 2013. Communications in Computer and Information Science, vol 370. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38865-1_33
Download citation
DOI: https://doi.org/10.1007/978-3-642-38865-1_33
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-38864-4
Online ISBN: 978-3-642-38865-1
eBook Packages: Computer ScienceComputer Science (R0)