On the characterization of the dipolar spin-spin interaction in molecular systems: A symbolic matrix element approach

1987 ◽  
Vol 141 (5) ◽  
pp. 391-396 ◽  
Author(s):  
James O. Jensen ◽  
David R. Yarkony
Keyword(s):  
Matrix Element ◽  
Spin Interaction ◽  
Molecular Systems ◽  
Element Approach ◽  
Symbolic Matrix

scholarly journals DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Da-Wei Li ◽  
Alexandar L. Hansen ◽  
Chunhua Yuan ◽  
Lei Bruschweiler-Li ◽  
Rafael Brüschweiler
Keyword(s):  
Neural Network ◽  
Nmr Spectra ◽  
Deep Neural Network ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Two Dimensional ◽  
Molecular Systems ◽  
Intrinsically Disordered ◽  
Identification And Characterization

AbstractThe analysis of nuclear magnetic resonance (NMR) spectra for the comprehensive and unambiguous identification and characterization of peaks is a difficult, but critically important step in all NMR analyses of complex biological molecular systems. Here, we introduce DEEP Picker, a deep neural network (DNN)-based approach for peak picking and spectral deconvolution which semi-automates the analysis of two-dimensional NMR spectra. DEEP Picker includes 8 hidden convolutional layers and was trained on a large number of synthetic spectra of known composition with variable degrees of crowdedness. We show that our method is able to correctly identify overlapping peaks, including ones that are challenging for expert spectroscopists and existing computational methods alike. We demonstrate the utility of DEEP Picker on NMR spectra of folded and intrinsically disordered proteins as well as a complex metabolomics mixture, and show how it provides access to valuable NMR information. DEEP Picker should facilitate the semi-automation and standardization of protocols for better consistency and sharing of results within the scientific community.

CAST: A new program package for the accurate characterization of large and flexible molecular systems

2014 ◽  
Vol 35 (24) ◽  
pp. 1801-1807 ◽  
Author(s):  
Christoph Grebner ◽  
Johannes Becker ◽  
Daniel Weber ◽  
Daniel Bellinger ◽  
Maxim Tafipolski ◽  
...  
Keyword(s):  
Program Package ◽  
Molecular Systems

scholarly journals Measurement of Spin Correlation intt¯Production Using a Matrix Element Approach

2011 ◽  
Vol 107 (3) ◽  
Author(s):  
V. M. Abazov ◽  
B. Abbott ◽  
B. S. Acharya ◽  
M. Adams ◽  
T. Adams ◽  
...  
Keyword(s):  
Matrix Element ◽  
Spin Correlation ◽  
Element Approach

Characterization of Electronic Properties in Complex Molecular Systems: Modeling of a Micropolarity Probe

2010 ◽  
Vol 114 (5) ◽  
pp. 1915-1924 ◽  
Author(s):  
Massimiliano Aschi ◽  
Antonella Fontana ◽  
Erika Maria Di Meo ◽  
Costantino Zazza ◽  
Andrea Amadei
Keyword(s):  
Electronic Properties ◽  
Systems Modeling ◽  
Molecular Systems

scholarly journals Characterization of a maternal type VI collagen in Xenopus embryos suggests a role for collagen in gastrulation.

1990 ◽  
Vol 111 (1) ◽  
pp. 271-278 ◽  
Author(s):  
A P Otte ◽  
D Roy ◽  
M Siemerink ◽  
C H Koster ◽  
F Hochstenbach ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Amino Acid ◽  
Matrix Element ◽  
Culture Medium ◽  
Collagen Type ◽  
Developmental Stages ◽  
Molecular Weights ◽  
Collagen Type Vi ◽  
Cell Layers

We characterized a novel extracellular matrix element that is present in the earliest developmental stages of Xenopus laevis, and is recognized by an mAb 3D7. Based on amino acid composition, breakdown patterns by bacterial collagenases, and the molecular weights of the components of the antigen (240, 200, and 140 kD), we found it very similar to mammalian collagen type VI. The antigen is evenly distributed in unfertilized eggs. Shortly after fertilization, it becomes localized intracellularly in the periphery of the cleaving embryo as well as in the extracellular spaces. During gastrulation, the antigen was localized in the cells lining the blastopore and in the extracellular space between the two cell layers, in the presumptive archenteron. When Fab elements of the 3D7 antibody were added to the culture medium, gastrulation was blocked, suggesting a role for the antigen in gastrulation movements.

scholarly journals A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

2021 ◽  
Author(s):  
Albert Smith ◽  
Alexander Vogel ◽  
Oskar Engberg ◽  
Peter Hildebrand ◽  
Daniel Huster
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membranes ◽  
Nmr Relaxation ◽  
Dynamics Simulation ◽  
Molecular Systems ◽  
Biological Interface ◽  
Novel Approach ◽  
Wide Range ◽  
Dynamic Landscape

Abstract Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report a novel approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use NMR relaxation and molecular dynamics simulation data for the characterization of lipid membranes, the most important biological interface. We develop a dynamics detector method that yields site-specific amplitudes, separated both by type and timescale of motion. This separation allows the detailed description of the dynamic landscape, which reveals vast differences in motion depending on molecular position. More generally, the method is applicable to a broad range of molecular systems, and can be adapted to other timescale-sensitive techniques.

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