Abstract
Protein function is mainly determined by its structure. For example, the interaction between ligands and receptors demands a match between their shapes. In this chapter we discuss morphological features of protein spatial structures using geometrical methods. The shape description of a binding pocket on the protein surface using geometrical tools is given, including a spatial polyhedron, the hypergraph and depth analysis. Furthermore, we generalize the rolling sphere method, and present several new concepts, such as the γ-accessible radius and γ-function in a spatial particle system, which connects with the biological concepts such as hydrophobicity using precise mathematical notions. We provide a recursive algorithm for the γ-function. The proof of the relative theorem and reasoning behind the computational formulas are given in the last section.
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© 2008 Springer-Verlag Berlin Heidelberg
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(2008). Analysis of the Morphological Features of Protein Spatial Structure. In: Theory and Mathematical Methods for Bioinformatics. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74891-5_14
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DOI: https://doi.org/10.1007/978-3-540-74891-5_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-74890-8
Online ISBN: 978-3-540-74891-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)