Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparison

EMBL-EBI, Cambridge, England, United Kingdom
Bioinformatics (Impact Factor: 4.98). 06/2005; 21(10):2347-55. DOI: 10.1093/bioinformatics/bti337
Source: PubMed


An increasing number of protein structures are being determined for which no biochemical characterization is available. The analysis of protein structure and function assignment is becoming an unexpected challenge and a major bottleneck towards the goal of well-annotated genomes. As shape plays a crucial role in biomolecular recognition and function, the examination and development of shape description and comparison techniques is likely to be of prime importance for understanding protein structure-function relationships.
A novel technique is presented for the comparison of protein binding pockets. The method uses the coefficients of a real spherical harmonics expansion to describe the shape of a protein's binding pocket. Shape similarity is computed as the L2 distance in coefficient space. Such comparisons in several thousands per second can be carried out on a standard linux PC. Other properties such as the electrostatic potential fit seamlessly into the same framework. The method can also be used directly for describing the shape of proteins and other molecules.
A limited version of the software for the real spherical harmonics expansion of a set of points in PDB format is freely available upon request from the authors. Binding pocket comparisons and ligand prediction will be made available through the protein structure annotation pipeline Profunc (written by Roman Laskowski) which will be accessible from the EBI website shortly.

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Available from: Abdullah Kahraman, Oct 04, 2015
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    • "SPHARM therefore have global spatial support, and each coefficient describes the general conformation of the shape of interest at different spatial scales. Applications of SPHARM include molecular surface modeling [50], [51], medical-shape analysis [52], and cellshape analysis [15], [16], [19], [53]. In the latter case, the function basis is formed of wavelets (hence its name), and are constructed by analogy to wavelets in the plane via appropriate spherical projections [17], [20], [54]. "
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    • "Moment-based methods can naturally control the resolution of the surface description , and physicochemical properties on the surface can be represented in the same way as surface shape. Thornton and her colleagues used spherical harmonics for describing binding pockets (Kahraman et al., 2007; Morris et al., 2005). In our earlier works, Pocket-Surfer, global pocket shape and the surface electrostatic potential are represented using 3D Zernike descriptors (3DZD; Chikhi et al., 2010). "
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    • "Another method is to describe hydrophobic features of the protein using turns in main chain atoms. Yet another approach is to use a Fourier shape descriptor technique (5, 6). "
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