Approximating deformation fields for the analysis of continuous
heterogeneity of biological macromolecules by 3D Zernike
polynomials

J 2021

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

HERREROS, David; Roy R LEDERMAN; James KRIEGER; Amaya JIMENEZ-MORENO; Marta MARTINEZ et al.

Základní údaje

Originální název

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

Autoři

HERREROS, David; Roy R LEDERMAN; James KRIEGER; Amaya JIMENEZ-MORENO; Marta MARTINEZ; David MYŠKA; David STŘELÁK; Jiří FILIPOVIČ; Ivet BAHAR; Jose Maria CARAZO a Carlos Oscar S SANCHEZ

Vydání

International Union of Crystallography Journals, online, 2021, 2052-2525

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.588

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14610/21:00122595

Organizační jednotka

Ústav výpočetní techniky

Klíčová slova anglicky

multi-dimensional scaling (MDS); 3D reconstruction and image processing; single-particle cryo-EM; spherical harmonics; Zernike polynomials; conformations

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 16. 5. 2022 15:08, Mgr. Alena Mokrá

Anotace

V originále

Structural biology has evolved greatly due to the advances introduced in fields like electron microscopy. This image-capturing technique, combined with improved algorithms and current data processing software, allows the recovery of different conformational states of a macromolecule, opening new possibilities for the study of its flexibility and dynamic events. However, the ensemble analysis of these different conformations, and in particular their placement into a common variable space in which the differences and similarities can be easily recognized, is not an easy matter. To simplify the analysis of continuous heterogeneity data, this work proposes a new automatic algorithm that relies on a mathematical basis defined over the sphere to estimate the deformation fields describing conformational transitions among different structures. Thanks to the approximation of these deformation fields, it is possible to describe the forces acting on the molecules due to the presence of different motions. It is also possible to represent and compare several structures in a low-dimensional mapping, which summarizes the structural characteristics of different states. All these analyses are integrated into a common framework, providing the user with the ability to combine them seamlessly. In addition, this new approach is a significant step forward compared with principal component analysis and normal mode analysis of cryo-electron microscopy maps, avoiding the need to select components or modes and producing localized analysis.

Návaznosti

EF16_013/0001802, projekt VaV

Název: CERIT Scientific Cloud

MUNI/A/1411/2019, interní kód MU

Název: Aplikovaný výzkum: softwarové architektury kritických infrastruktur, bezpečnost počítačových systémů, zpracování přirozeného jazyka a jazykové inženýrství, vizualizaci velkých dat a rozšířená realita.

Investor: Masarykova univerzita, Aplikovaný výzkum: softwarové architektury kritických infrastruktur, bezpečnost počítačových systémů, zpracování přirozeného jazyka a jazykové inženýrství, vizualizaci velkých dat a rozšířená realita., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

HERREROS, David; Roy R LEDERMAN; James KRIEGER; Amaya JIMENEZ-MORENO; Marta MARTINEZ; David MYŠKA; David STŘELÁK; Jiří FILIPOVIČ; Ivet BAHAR; Jose Maria CARAZO a Carlos Oscar S SANCHEZ. Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. International Union of Crystallography Journals. online, 2021, roč. 8, č. 6, s. 992-1005. ISSN 2052-2525. Dostupné z: https://doi.org/10.1107/S2052252521008903.

@article{1798284,
   author = {Herreros, David and Lederman, Roy R and Krieger, James and JimenezandMoreno, Amaya and Martinez, Marta and Myška, David and Střelák, David and Filipovič, Jiří and Bahar, Ivet and Carazo, Jose Maria and Sanchez, Carlos Oscar S},
   article_location = {online},
   article_number = {6},
   doi = {https://doi.org/10.1107/S2052252521008903},
   keywords = {multi-dimensional scaling (MDS); 3D reconstruction and image processing; single-particle cryo-EM; spherical harmonics; Zernike polynomials; conformations},
   language = {eng},
   issn = {2052-2525},
   journal = {International Union of Crystallography Journals},
   title = {Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials},
   url = {https://journals.iucr.org/m/issues/2021/06/00/eh5012/index.html},
   volume = {8},
   year = {2021}
}

TY  - JOUR
ID  - 1798284
AU  - Herreros, David - Lederman, Roy R - Krieger, James - Jimenez-Moreno, Amaya - Martinez, Marta - Myška, David - Střelák, David - Filipovič, Jiří - Bahar, Ivet - Carazo, Jose Maria - Sanchez, Carlos Oscar S
PY  - 2021
TI  - Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials
JF  - International Union of Crystallography Journals
VL  - 8
IS  - 6
SP  - 992-1005
EP  - 992-1005
SN  - 20522525
KW  - multi-dimensional scaling (MDS)
KW  - 3D reconstruction and image processing
KW  - single-particle cryo-EM
KW  - spherical harmonics
KW  - Zernike polynomials
KW  - conformations
UR  - https://journals.iucr.org/m/issues/2021/06/00/eh5012/index.html
N2  - Structural biology has evolved greatly due to the advances introduced in fields like electron microscopy. This image-capturing technique, combined with improved algorithms and current data processing software, allows the recovery of different conformational states of a macromolecule, opening new possibilities for the study of its flexibility and dynamic events. However, the ensemble analysis of these different conformations, and in particular their placement into a common variable space in which the differences and similarities can be easily recognized, is not an easy matter. To simplify the analysis of continuous heterogeneity data, this work proposes a new automatic algorithm that relies on a mathematical basis defined over the sphere to estimate the deformation fields describing conformational transitions among different structures. Thanks to the approximation of these deformation fields, it is possible to describe the forces acting on the molecules due to the presence of different motions. It is also possible to represent and compare several structures in a low-dimensional mapping, which summarizes the structural characteristics of different states. All these analyses are integrated into a common framework, providing the user with the ability to combine them seamlessly. In addition, this new approach is a significant step forward compared with principal component analysis and normal mode analysis of cryo-electron microscopy maps, avoiding the need to select components or modes and producing localized analysis.
ER  -

HERREROS, David; Roy R LEDERMAN; James KRIEGER; Amaya JIMENEZ-MORENO; Marta MARTINEZ; David MYŠKA; David STŘELÁK; Jiří FILIPOVIČ; Ivet BAHAR; Jose Maria CARAZO a Carlos Oscar S SANCHEZ. Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. \textit{International Union of Crystallography Journals}. online, 2021, roč.~8, č.~6, s.~992-1005. ISSN~2052-2525. Dostupné z: https://doi.org/10.1107/S2052252521008903.

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