Spinor product computations for protein conformations

Journal of Computational Chemistry
Pieter Chys, Pablo Chacón

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.

References

Dec 19, 2001·Journal of Biomechanics·Sahan S Hiniduma Udugama Gamage, Joan Lasenby
Nov 6, 2003·Protein Engineering·Carlos Alvarado, Kazem Kazerounian
Sep 18, 2004·Journal of Computational Chemistry·Evangelos A CoutsiasKen A Dill
May 18, 2005·Journal of Computational Chemistry·Jerod ParsonsCharlie E M Strauss
Jan 24, 2006·Journal of Chemical Information and Modeling·Vicky Choi
Jan 23, 1987·Science·A T BrüngerM Karplus
Nov 17, 2007·Nature Protocols·Axel T Brunger
Mar 19, 2008·The Journal of Chemical Physics·Pieter Chys

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Citations

May 7, 2016·Nucleic Acids Research·José Ramón López-BlancoPablo Chacón
Jul 21, 2020·Journal of Computational Chemistry·Mahsa BayatiJaydeep P Bardhan
Mar 12, 2013·Journal of Chemical Theory and Computation·Pieter Chys, Pablo Chacón

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