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

0533113 - ÚOCHB 2021 RIV DE eng J - Journal Article
Giassa, I.C. - Vavrinská, A. - Zelinka, J. - Šebera, Jakub - Sychrovský, Vladimír - Boelens, R. - Fiala, R. - Trantírek, L.
HERMES – A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids.
ChemPlusChem. Roč. 85, č. 9 (2020), s. 2177-2185. ISSN 2192-6506. E-ISSN 2192-6506
R&D Projects: GA ČR(CZ) GA19-13436S
Institutional support: RVO:61388963
Keywords : field-induced residual dipolar couplings * magnetic susceptibility anisotropy * NMR * nucleic acids * prediction software
OECD category: Physical chemistry
Impact factor: 2.863, year: 2020
Method of publishing: Limited access
https://doi.org/10.1002/cplu.202000505

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.
Permanent Link: http://hdl.handle.net/11104/0311738