The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S² to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite...
[NMR paper] Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates
Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates
Simultaneous prediction of the molecular response properties, such as polarizability and the NMR shielding constant, at a low computational cost is an unresolved issue. We propose to combine a linear-scaling generalized energy-based fragmentation (GEBF) method and deep learning (DL) with both molecular and atomic information-theoretic approach (ITA) quantities as effective descriptors. In GEBF, the total molecular polarizability can be assembled as a linear...
[NMR paper] Introducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
Introducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
Related Articles Introducing the CSP Analyzer: A novel Machine Learning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening.
Comput Struct Biotechnol J. 2020;18:603-611
Authors: Fino R, Byrne R, Softley CA, Sattler M, Schneider G, Popowicz GM
Abstract
NMR-based screening, especially fragment-based drug discovery is a...
[NMR paper] Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Related Articles Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Chemistry. 2017 May 15;:
Authors: Smith LJ, Athill R, van Gunsteren WF, Hansen N
Abstract
At low pH human growth hormone (hGH) adopts a partially folded state...
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[NMR paper] Contact model for the prediction of NMR N-H order parameters in globular proteins.
Contact model for the prediction of NMR N-H order parameters in globular proteins.
Related Articles Contact model for the prediction of NMR N-H order parameters in globular proteins.
J Am Chem Soc. 2002 Oct 30;124(43):12654-5
Authors: Zhang F, Brüschweiler R
An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the...
Prediction of order parameters based on protein NMR structure ensemble and machine learning
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