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.

Basic information

Original name

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

Authors

GIASSA, Ilektra-Chara (300 Greece, belonging to the institution), Andrea VAVRINSKÁ, Jiří ZELINKA (203 Czech Republic, belonging to the institution), Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Rolf BOELENS, Radovan FIALA (203 Czech Republic, belonging to the institution) and Lukáš TRANTÍREK (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.863

RIV identification code

RIV/00216224:14740/20:00117855

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000573610000024

Keywords in English

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

Abstract

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.

Links

NV19-08-00450, research and development project

Name: 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: Ministry of Health of the CR

90127, large research infrastructures

Name: CIISB II

Citovat

GIASSA, Ilektra-Chara, Andrea VAVRINSKÁ, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Rolf BOELENS, Radovan FIALA and 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, vol. 85, No 9, p. 2177-2185. ISSN 2192-6506. Available from: 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 and 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, vol.~85, No~9, p.~2177-2185. ISSN~2192-6506. Available from: https://dx.doi.org/10.1002/cplu.202000505.

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