Volume fractal dimensionality: a useful parameter for measuring the complexity of 3D protein spatial structures

ABSTRACT

A quantitative measure for estimating the complexity of 3D protein is proposed. The measurement is based on the fractal features of protein structures. A practical method for evaluating the volume fractal dimensionality (VFD) is described. Our investigations on large data sets from PDB show that similar protein shapes have close VFD and VFD may therefore be used as a token of evolutional proteins, and for protein prediction.

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INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

General Terms:
Algorithms, Measurement

Keywords:
dimensionality (VFD), protein structure, quantitative measure, volume fractal