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Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces

David Ritchie 1, * Graham Kemp
* Corresponding author
Abstract : A procedure that rapidly generates an approximate parametric representation of macromolecular surface shapes is described. The parametrization is expressed as an expansion of real spherical harmonic basis functions. The advantage of using a parametric representation is that a pair of surfaces can be matched by using a quasi-Newton algorithm to minimize a suitably chosen objective function. Spherical harmonics are a natural and convenient choice of basis function when the task is one of search in a rotational search space. In particular, rotations of a molecular surface can be simulated by rotating only the harmonic expansion coefficients. This rotational property is applied for the first time to the 3-dimensional molecular similarity problem in which a pair of similar macromolecular surfaces are to be maximally superposed. The method is demonstrated with the superposition of antibody heavy chain variable domains. Special attention is given to computational efficiency. The spherical harmonic expansion coefficients are determined using fast surface sampling and integration schemes based on the tessellation of a regular icosahedron. Low resolution surfaces can be generated and displayed in under 10 s and a pair of surfaces can be maximally superposed in under 3 s on a contemporary workstation.
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https://hal.inria.fr/inria-00434275
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Submitted on : Saturday, November 21, 2009 - 5:14:02 PM
Last modification on : Tuesday, November 28, 2017 - 3:18:04 PM

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David Ritchie, Graham Kemp. Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. Journal of Computational Chemistry, Wiley, 1999, 20 (4), pp.383-395. ⟨10.1002/(SICI)1096-987X(199903)20:4<383::AID-JCC1>3.0.CO;2-M⟩. ⟨inria-00434275⟩

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