Abstract
Macromolecular structural analysis has been used for a long time, in particular for proteins, with the aim of correlating three dimensional structures with possible functions and interactions. An innovative approach is to tackle these aspects by working on macromolecular surfaces instead of using amino acid or atomic configurations directly, because protein interaction is mainly driven by the macromolecular external characteristics. However, it is difficult to work with surfaces because applications for molecular visualization lack appropriate functions to manipulate these data structures properly. In this paper we describe a visualization pipeline to represent molecular surfaces in three-dimensional space. The pipeline relies on the Visualization Toolkit libraries, and provides a high level functions and easy user interface. This software has been developed in the context of a surface analysis project, but its classes and methods can be used and integrated in a wide range of applications.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Watson, J.D., Laskowski, R.A., Thornton, J.M.: Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol. 15, 275–284 (2005)
Camacho, C.J., Vajda, S.: Protein-protein association kinetics and protein docking. Curr. Opin. Struct. Biol. 12, 36–40 (2002)
Merelli, I., Cozzi, P., Milanesi, L., D’Agostino, D., Clematis, A.: Images based system for surface matching in macromulecular screening. In: 2008 IEEE International Conference on Bioinformatics and Biomedicine (in press, 2008)
Schroeder, W.J., Avila, L.S., Hoffman, W.: Visualizing with VTK: a tutorial. Computer Graphics and Application 20, 20–27 (2000)
Schroeder, W.J., Martin, K., Lorensen, B.: The Visualization Toolkit - An object Oriented Approach to 3D Graphics. Kitware (2004)
Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., Lopez, R.: InterProScan: protein domains identifier. Nucleic Acids Res. 33(Web Server issue), W116–W120 (2005)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Res. 28(1), 235–242 (2000)
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
Cozzi, P., Merelli, I., Milanesi, L. (2009). A Visualization ToolKit Based Application for Representing Macromolecular Surfaces. In: Masulli, F., Tagliaferri, R., Verkhivker, G.M. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2008. Lecture Notes in Computer Science(), vol 5488. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02504-4_26
Download citation
DOI: https://doi.org/10.1007/978-3-642-02504-4_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02503-7
Online ISBN: 978-3-642-02504-4
eBook Packages: Computer ScienceComputer Science (R0)