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J Comput Chem. 2012 Aug 5;33(21):1717-29. doi: 10.1002/jcc.23002. Epub 2012 May 8.

Spinor product computations for protein conformations.

Author information

1
Structural Bioinformatics Group, Department of Biological Chemical Physics, Institute of Physical Chemistry Rocasolano, Consejo Superior de Investigaciones Cientificas, Madrid, Spain.

Abstract

Spinor operators in geometric algebra (GA) can efficiently describe conformational changes of proteins by ordered products that act on individual bonds and represent their net rotations. Backward propagation through the protein backbone yields all rotational spinor axes in advance allowing the efficient computation of atomic coordinates from internal coordinates. The introduced mathematical framework enables to efficiently manipulate and generate protein conformations to any arbitrary degree. Moreover, several new formulations in the context of rigid body motions are added. Emphasis is placed on the intimate relationship between spinors and quaternions, which can be recovered from within the GA approach. The spinor methodology is implemented and tested versus the state of the art algorithms for both protein construction and coordinate updating. Spinor calculations have a smaller computational cost and turn out to be slightly faster than current alternatives.

PMID:
22565650
DOI:
10.1002/jcc.23002
[Indexed for MEDLINE]

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