[HTML][HTML] Simulation of FRET dyes allows quantitative comparison against experimental data

I Reinartz, C Sinner, D Nettels… - The Journal of …, 2018 - pubs.aip.org
Fully understanding biomolecular function requires detailed insight into the systems'
structural dynamics. Powerful experimental techniques such as single molecule Förster …

Rapid interpretation of small-angle X-ray scattering data

M Weiel, I Reinartz, A Schug - PLoS computational biology, 2019 - journals.plos.org
The fundamental aim of structural analyses in biophysics is to reveal a mutual relation
between a molecule's dynamic structure and its physiological function. Small-angle X-ray …

Simulating protein fold switching by replica exchange with tunneling

NA Bernhardt, W Xi, W Wang… - Journal of chemical …, 2016 - ACS Publications
Recent experiments suggest that an amino acid sequence encodes not only the native fold
of a protein but also other forms that are essential for its function or are important during …

Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies

M Shibata, X Lin, JN Onuchic, K Yura, RR Cheng - Biophysical Journal, 2024 - cell.com
DNA-binding response regulators (DBRRs) are a broad class of proteins that operate in
tandem with their partner kinase proteins to form two-component signal transduction …

Formation of a secretion-competent protein complex by a dynamic wrap-around binding mechanism

AA Gupta, I Reinartz, G Karunanithy, A Spilotros… - Journal of molecular …, 2018 - Elsevier
Bacterial virulence is typically initiated by translocation of effector or toxic proteins across
host cell membranes. A class of gram-negative pathogenic bacteria including Yersinia …

Revealing the global map of protein folding space by large-scale simulations

C Sinner, B Lutz, A Verma, A Schug - The Journal of Chemical Physics, 2015 - pubs.aip.org
The full characterization of protein folding is a remarkable long-standing challenge both for
experiment and simulation. Working towards a complete understanding of this process, one …

FRET dyes significantly affect SAXS intensities of proteins

I Reinartz, M Weiel, A Schug - Israel journal of chemistry, 2020 - Wiley Online Library
Structural analyses in biophysics aim at revealing a relationship between a molecule's
dynamic structure and its physiological function. Förster resonance energy transfer (FRET) …

Native structure-based modeling and simulation of biomolecular systems per mouse click

B Lutz, C Sinner, S Bozic, I Kondov, A Schug - BMC bioinformatics, 2014 - Springer
Background Molecular dynamics (MD) simulations provide valuable insight into
biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high …

Potential Self-Peptide Inhibitors of the SARS-CoV-2 Main Protease

A Banerjee, S Gosavi - The Journal of Physical Chemistry B, 2023 - ACS Publications
The SARS-CoV-2 main protease (Mpro) plays an essential role in viral replication, cleaving
viral polyproteins into functional proteins. This makes Mpro an important drug target. Mpro …

Characterising the combined eects of cytochrome P450 missense variants within the star allele nomenclature

N Khoza - wiredspace.wits.ac.za
Genetic variations in Cytochrome P450 (CYP) enzymes shape drug responses. However,
many CYP haplotypes (star alleles) lack functional annotations, posing a barrier to under …