PyEMMA 2: A software package for estimation, validation, and analysis of Markov models

MK Scherer, B Trendelkamp-Schroer… - Journal of chemical …, 2015 - ACS Publications
Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …

The metastable states of proteins

DK Ghosh, A Ranjan - Protein Science, 2020 - Wiley Online Library
The intriguing process of protein folding comprises discrete steps that stabilize the protein
molecules in different conformations. The metastable state of protein is represented by …

GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules

M Ghorbani, S Prasad, JB Klauda… - The Journal of Chemical …, 2022 - pubs.aip.org
Finding a low dimensional representation of data from long-timescale trajectories of
biomolecular processes, such as protein folding or ligand–receptor binding, is of …

Multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations

SK Sadiq, A Muñiz Chicharro, P Friedrich… - Journal of Chemical …, 2021 - ACS Publications
We develop an approach to characterize the effects of gating by a multiconformation protein
consisting of macrostate conformations that are either accessible or inaccessible to ligand …

Phospho‐dependent signaling during the general stress response by the atypical response regulator and ClpXP adaptor RssB

J Schwartz, J Son, C Brugger… - Protein …, 2021 - Wiley Online Library
In the model organism Escherichia coli and related species, the general stress response
relies on tight regulation of the intracellular levels of the promoter specificity subunit RpoS …

[HTML][HTML] Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana

O Otrusinová, G Demo, P Padrta, Z Jaseňáková… - Journal of Biological …, 2017 - ASBMB
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli,
including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we …

[HTML][HTML] 细菌反应调节蛋白RR468 磷酸化和去磷酸化关键位点的NMR 研究

王丹, 刘乙祥, 寇新慧, 刘买利, 姜凌 - 波谱学杂志, 2017 - html.rhhz.net
反应调节蛋白是细菌双组分信号转导系统的重要组分, 用于传递来自组氨酸激酶的信号并产生
适应性反应. 在整个信号转导过程中, 反应调节蛋白的磷酸化和去磷酸化最终决定了该系统的 …

Optimising nanopores for DNA sequencing: A computational perspective

P Rattu - 2023 - eprints.soton.ac.uk
Nanopore DNA sequencing is a well-established technology that has accelerated
advancements in many fields, including medical research. Over the years, research has …

[PDF][PDF] Olga Otrusinová1, 2, Gabriel Demo1, 3, Petr Padrta1, 2, Zuzana Jaseňáková1, 2, Blanka Pekárová1, 2, Zuzana Gelová1, 2, Agnieszka Szmitkowska1, 2, Pavel …

M Wimmerová, J Hejátko, L Žídek - 2017 - researchgate.net
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli,
including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we …