HermiteFit: fast‐fitting atomic structures into a low‐resolution density map using three‐dimensional orthogonal Hermite functions. (1st August 2014)

• Record Type: Journal Article
• Authors: Derevyanko, Georgy; Grudinin, Sergei
• Is Part Of: Acta crystallographica. Volume 70:Part 8(2014:Aug.)
• Page Start: 2069
• Page End: 2084
• Publication Date: 2014-08-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004714011493
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p> <italic>HermiteFit</italic>, a novel algorithm for fitting a protein structure into a low‐resolution electron‐density map, is presented. The algorithm accelerates the rotation of the Fourier image of the electron density by using three‐dimensional orthogonal Hermite functions. As part of the new method, an algorithm for the rotation of the density in the Hermite basis and an algorithm for the conversion of the expansion coefficients into the Fourier basis are presented. <italic>HermiteFit</italic> was implemented using the cross‐correlation or the Laplacian‐filtered cross‐correlation as the fitting criterion. It is demonstrated that in the Hermite basis the Laplacian filter has a particularly simple form. To assess the quality of density encoding in the Hermite basis, an analytical way of computing the crystallographic <italic>R</italic> factor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods, <italic>ADP_EM</italic> and <italic>colores</italic> from the <italic>Situs</italic> package. <italic>HermiteFit</italic> will be made available at <ext-link ext-link-type="uri" xlink:href="http://nano-d.inrialpes.fr/software/HermiteFit" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">http://nano‐d.inrialpes.fr/software/HermiteFit</ext-link> or upon request from the authors.</p> </abstract>