Journal Article

FZJ-2015-04433

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions.

Derevyanko, G.FZJ* ; Grudinin, S. (Corresponding Author)

2014
Munksgaard Copenhagen

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Please use a persistent id in citations: doi:10.1107/S1399004714011493

Abstract: HermiteFit, 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. HermiteFit 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 R factor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods, ADP_EM and colores from the Situs package. HermiteFit will be made available at http://nano-d.inrialpes.fr/software/HermiteFit or upon request from the authors.

Keyword(s): Chaperonin 60 ; Conotoxins

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Contributing Institute(s):

1. Strukturbiochemie (ICS-6)

Research Program(s):

1. 452 - Structural Biology (POF2-452) (POF2-452)

Appears in the scientific report 2015

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Database coverage:
; BIOSIS Previews ; Current Contents - Life Sciences ; IF >= 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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