Flexible Multi-scale Fitting of Atomic Structures into Low-resolution Electron Density Maps with Elastic Network Normal Mode Analysis

2004 ◽  
Vol 337 (4) ◽  
pp. 985-999 ◽  
Author(s):  
Florence Tama ◽  
Osamu Miyashita ◽  
Charles L. Brooks
Keyword(s):  
Electron Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Low Resolution ◽  
Elastic Network ◽  
Atomic Structures ◽  
Multi Scale ◽  
Density Maps ◽  
Resolution Electron

A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes

2019 ◽  
Vol 21 (8) ◽  
pp. 4359-4366 ◽  
Author(s):  
D. Vijay Anand ◽  
Zhenyu Meng ◽  
Kelin Xia
Keyword(s):  
Normal Mode ◽  
Network Model ◽  
Material Properties ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Particle Model ◽  
Elastic Network Model ◽  
Elastic Network ◽  
Virtual Particle ◽  
Biomolecular Complexes

The CMVP-ENM for virus normal mode analysis. With a special ratio parameter, CMVP-ENM can characterize the multi-material properties of biomolecular complexes and systematically enhance or suppress the modes for different components.

scholarly journals HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions

2014 ◽  
Vol 70 (8) ◽  
pp. 2069-2084 ◽  
Author(s):  
Georgy Derevyanko ◽  
Sergei Grudinin
Keyword(s):  
Electron Density ◽  
Cross Correlation ◽  
Three Dimensional ◽  
Hermite Functions ◽  
Low Resolution ◽  
Atomic Structures ◽  
Resolution Electron ◽  
Laplacian Filter ◽  
Density Map ◽  
Electron Density Map

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.HermiteFitwas 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 crystallographicRfactor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods,ADP_EMandcoloresfrom theSituspackage.HermiteFitwill be made available at http://nano-d.inrialpes.fr/software/HermiteFit or upon request from the authors.

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