Results 61 to 70 of about 15,544 (215)

Refinement of amino‐acid conformation vs. difference density maps in time‐resolved serial femtosecond crystallography data analysis

FEBS Open Bio, EarlyView.
The dFoCC pipeline starts with observed DED and resting‐state coordinates, which are then used to generate a library of triggered states. Correlation analysis of the calculated DED features of each candidate vs observed DED permits quantitative evaluation of candidate structural quality.
Meng Iao Fong, Yuhei Hosokawa, Lars Oliver Essen, Manuel Maestre‐Reyna   +3 more
wiley   +1 more source

Support for Multiscale Simulations with Molecular Dynamics

Procedia Computer Science, 2013
AbstractWe present a reusable solution that supports users in combining single-scale models to create a multiscale application. Our approach applies several multiscale programming tools to allow users to compose multiscale applications using a graphical interface, and provides an easy way to execute these multiscale applications on international ...
Katarzyna Rycerz, Eryk Ciepiela, Grzegorz Dyk, Derek Groen, Tomasz Gubala, Daniel Harezlak, Maciej Pawlik, James J. Suter, Stefan J. Zasada, Peter V. Coveney, Marian Bubak   +10 more
openaire   +1 more source

Molecular characterization of covRS mutations in M1UK Streptococcus pyogenes

FEBS Open Bio, EarlyView.
Group A Streptococcus (GAS) acquires covRS mutations driving a hypervirulent bacterial state, frequently associated with invasive disease‐like necrotizing fasciitis. We demonstrate that the newly emerged M1UK GAS lineage can also acquire these mutations.
Jarrad Pritchard, Emma‐Jayne Proctor, Jiawa Wang, Nikolas P. Johnston, Andrew Hayes, Georgia McCorkell, Haibo Yu, Jai Tree, Mark R. Davies, Mark J. Walker, Ronald Sluyter, Stephan Brouwer, Martina L. Sanderson‐Smith   +12 more
wiley   +1 more source

The Activation and Selectivity of the Legionella RavD Deubiquitinase

Frontiers in Molecular Biosciences, 2021
Eric Schulze-Niemand, Eric Schulze-Niemand, Michael Naumann, Matthias Stein   +3 more
doaj   +1 more source

StreaMD: the toolkit for high-throughput molecular dynamics simulations

Journal of Cheminformatics
Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein–ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing ...
Aleksandra Ivanova, Olena Mokshyna, Pavel Polishchuk   +2 more
doaj   +1 more source

Machine Learning with and for Molecular Dynamics Simulations

CHIMIA, 2019
From simple clustering techniques to more sophisticated neural networks, the use of machine learning has become a valuable tool in many fields of chemistry in the past decades.
Sereina Riniker, Shuzhe Wang, Patrick Bleiziffer, Lennard Böselt, Carmen Esposito   +4 more
doaj   +1 more source

Transcripts enriched in codons that trigger P‐site tRNA‐mediated mRNA decay possess stable mRNA

FEBS Open Bio, EarlyView.
PTMD codons were first described by Mendel et al. as mediators of an mRNA decay pathway dependent on the human protein CNOT3, homologous to yeast Not5. Our findings confirm that PTMD codons destabilize transcripts; however, unlike in yeast, the human pathway specifically targets and slightly destabilizes primarily stable mRNAs.
Rodolfo Lopes Carneiro, Fernando Lucas Palhano   +1 more
wiley   +1 more source

Pathways and pitfalls: a qualitative study of student experiences in biomedical science education

FEBS Open Bio, EarlyView.
Biomedical science students from underrepresented backgrounds face barriers including financial strain, disrupted laboratory access and cultural exclusion. Peer networks provide vital support when institutional systems are difficult to navigate. To create inclusive learning environments and achieve academic success, educators should blend active, hands‐
Olivia J. Russell, Cassy Ross, Panagiota S. Filippou, Bruno Silvester Lopes, Dominic Gilchrist, Paul Dean, Kamar Ameen‐Ali, Tora K. Smulders‐Srinivasan, Ahmad A. Khundakar   +8 more
wiley   +1 more source

Neurochemical Endpoints to Inform Early‐Stage Trials of Spinocerebellar Ataxia 2 and 3 in a Multisite Setting

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Neurochemical levels measured by brain MR spectroscopy (MRS) have been proposed as endpoints for clinical trials in early‐stage spinocerebellar ataxia (SCA) trials. We tested their trial‐readiness by quantifying neurochemicals in three affected brain regions in early‐stage cohorts of SCA2 and SCA3, examining their reproducibility in ...
James M. Joers, Yaqiao Wei, Dinesh K. Deelchand, Adam Berrington, Young Woo Park, Guita Banan, Michal Povazan, Jens T. Rosenberg, André J. W. van der Kouwe, Tetsuo Ashizawa, Khalaf O. Bushara, Chiadi U. Onyike, Sub H. Subramony, Jeremy D. Schmahmann, Brian J. Soher, Peter B. Barker, Thomas H. Mareci, Eva‐Maria Ratai, Lynn E. Eberly, Gülin Öz   +19 more
wiley   +1 more source

Continuous Finite Element Methods of Molecular Dynamics Simulations

Modelling and Simulation in Engineering, 2015
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems.
Qiong Tang, Luohua Liu, Yujun Zheng
doaj   +1 more source