HERMES - A Software Tool for the Prediction and Analysis of
Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic
Acids

J 2020

HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids

GIASSA, Ilektra-Chara, Andrea VAVRINSKÁ, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ et. al.

Základní údaje

Originální název

HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids

Autoři

GIASSA, Ilektra-Chara (300 Řecko, domácí), Andrea VAVRINSKÁ, Jiří ZELINKA (203 Česká republika, domácí), Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Rolf BOELENS, Radovan FIALA (203 Česká republika, domácí) a Lukáš TRANTÍREK (203 Česká republika, garant, domácí)

Vydání

ChemPlusChem, Weinheim, Wiley - Verlag Chemie, 2020, 2192-6506

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.863

Kód RIV

RIV/00216224:14740/20:00117855

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/cplu.202000505

UT WoS

000573610000024

Klíčová slova anglicky

field-induced residual dipolar couplings; magnetic susceptibility anisotropy; NMR; nucleic acids; prediction software

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 10. 2024 14:15, Ing. Martina Blahová

Anotace

V originále

Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.

Návaznosti

NV19-08-00450, projekt VaV

Název: Atomárně rozlišená NMR spektroskopie in vivo jako nástroj pro biologické testování terapeuticky významných cílů v genomové ne-kanonické DNA a jejich interakcí s léčivy ve fenotypově diverzifikovaných nádorových buňkách.

Investor: Ministerstvo zdravotnictví ČR, Atomically resolved in vivo NMR spectroscopy as a novel tool for biological testing of therapeutically important genomic non-canonical DNA targets and their interactions with drugs in phenotypically diversified cancer cells.

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

GIASSA, Ilektra-Chara, Andrea VAVRINSKÁ, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Rolf BOELENS, Radovan FIALA a Lukáš TRANTÍREK. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. ChemPlusChem. Weinheim: Wiley - Verlag Chemie, 2020, roč. 85, č. 9, s. 2177-2185. ISSN 2192-6506. Dostupné z: https://dx.doi.org/10.1002/cplu.202000505.

@article{1729960,
   author = {Giassa, IlektraandChara and Vavrinská, Andrea and Zelinka, Jiří and Šebera, Jakub and Sychrovský, Vladimír and Boelens, Rolf and Fiala, Radovan and Trantírek, Lukáš},
   article_location = {Weinheim},
   article_number = {9},
   doi = {http://dx.doi.org/10.1002/cplu.202000505},
   keywords = {field-induced residual dipolar couplings; magnetic susceptibility anisotropy; NMR; nucleic acids; prediction software},
   language = {eng},
   issn = {2192-6506},
   journal = {ChemPlusChem},
   title = {HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids},
   url = {https://doi.org/10.1002/cplu.202000505},
   volume = {85},
   year = {2020}
}

TY  - JOUR
ID  - 1729960
AU  - Giassa, Ilektra-Chara - Vavrinská, Andrea - Zelinka, Jiří - Šebera, Jakub - Sychrovský, Vladimír - Boelens, Rolf - Fiala, Radovan - Trantírek, Lukáš
PY  - 2020
TI  - HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids
JF  - ChemPlusChem
VL  - 85
IS  - 9
SP  - 2177-2185
EP  - 2177-2185
PB  - Wiley - Verlag Chemie
SN  - 21926506
KW  - field-induced residual dipolar couplings
KW  - magnetic susceptibility anisotropy
KW  - NMR
KW  - nucleic acids
KW  - prediction software
UR  - https://doi.org/10.1002/cplu.202000505
L2  - https://doi.org/10.1002/cplu.202000505
N2  - Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.
ER  -

GIASSA, Ilektra-Chara, Andrea VAVRINSKÁ, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Rolf BOELENS, Radovan FIALA a Lukáš TRANTÍREK. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. \textit{ChemPlusChem}. Weinheim: Wiley - Verlag Chemie, 2020, roč.~85, č.~9, s.~2177-2185. ISSN~2192-6506. Dostupné z: https://dx.doi.org/10.1002/cplu.202000505.

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