Results 81 to 90 of about 1,164,562 (348)

Molecular Dynamics Simulation for Membrane Fusion. [PDF]

Methods Mol Biol
The soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein complex drives membrane fusion, and this process is further aided by accessory proteins, including complexin and α-synuclein. To understand the molecular mechanism underlying membrane fusion, we introduce an all-atom molecular dynamics (MD) simulation method. This
Tyoe O, Zhang K, Diao J.
europepmc   +4 more sources

Molecular dynamics simulation of methane hydrate dissociation by depressurisation

, 2013
Methane (CH4) hydrate dissociation and the mechanism by depressurisation are investigated by molecular dynamics (MD) simulation. The hydrate decomposition processes are studied by the vacuum removal method' and the normal method.
Li, Bo, Chen, ZhaoYang, Xu, ChunGang, Li, XiaoSen, Yan, KeFeng   +4 more
core   +1 more source

Exon 7 splicing of ERα predicts poor prognosis and increases phenotypic heterogeneity in luminal a subtype breast cancer

FEBS Open Bio, EarlyView.
ERα splice variant ERα∆7 lacks the C‐terminus, and its expression may change phenotypes of breast cancers. Our results showed that ERα∆7 is found in the luminal A subtype, and elevated ERα∆7 levels are linked to improved cell survival with lower proliferation and migration.
Long Wai Tsui, Taobo Hu, Thomson Christian Husein, Wai Hei Shek, Bingrong Chen, Depeng Wang, Shu Wang, Weichuan Yu, Xiaodan Fan, Mengping Long, Toyotaka Ishibashi   +10 more
wiley   +1 more source

Analysing the significance of small conformational changes and low occupancy states in serial crystallographic data

FEBS Open Bio, EarlyView.
This protocol paper outlines methods to establish the success of a time‐resolved serial crystallographic experiment, by means of statistical analysis of timepoint data in reciprocal space and models in real space. We show how to amplify the signal from excited states to visualise structural changes in successful experiments.
Jake Hill, Yelyzaveta Pulnova, Elke De Zitter, Helen M. Ginn, Briony A. Yorke   +4 more
wiley   +1 more source

Molecular Dynamics Simulation of Biomolecular Systems

CHIMIA, 2001
The group for computer-aided chemistry at the ETH Zürich focuses its research on the development of methodology to simulate the behavior of biomolecular systems and the use of simulation techniques to analyze and understand biomolecular ...
Wilfred van Gunsteren, Thereza Soares, Lukas Schuler, Jed Pitera, Christine Peter, Chris Oostenbrink, Tomas Hansson, Alice Glättli, Peter Gee, Xavier Daura, Markus Christen, Indira Chandrasekhar, Roland Bürgi, Dirk Bakowies, Haibo Yu   +14 more
doaj  

Molecular dynamics simulations of polymerisation and crystallisation at constant chemical potential

, 2020
To investigate the complex process of polymer crystallisation during polymerisation, we develop a molecular dynamics (MD) simulation method with dynamic insertion and removal of comonomers in the simulation box.
Chen, Wei, Ren, Ying
core   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

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

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

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