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Jonathan Barnoud
Jonathan Barnoud
Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS) Universidade de Santiago de
Verified email at usc.es
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Year
MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations
RJ Gowers, M Linke, J Barnoud, TJE Reddy, MN Melo, SL Seyler, ...
Los Alamos National Lab.(LANL), Los Alamos, NM (United States), 2019
10292019
Martini 3: a general purpose force field for coarse-grained molecular dynamics
PCT Souza, R Alessandri, J Barnoud, S Thallmair, I Faustino, ...
Nature methods 18 (4), 382-388, 2021
5872021
Polystyrene nanoparticles perturb lipid membranes
G Rossi, J Barnoud, L Monticelli
The journal of physical chemistry letters 5 (1), 241-246, 2014
3222014
Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers
N Castillo, L Monticelli, J Barnoud, DP Tieleman
Chemistry and physics of lipids 169, 95-105, 2013
1352013
A coarse-grained MARTINI model of polyethylene glycol and of polyoxyethylene alkyl ether surfactants
G Rossi, PFJ Fuchs, J Barnoud, L Monticelli
The Journal of Physical Chemistry B 116 (49), 14353-14362, 2012
1152012
Protein flexibility in the light of structural alphabets
P Craveur, AP Joseph, J Esque, TJ Narwani, F Noël, N Shinada, ...
Frontiers in molecular biosciences 2, 20, 2015
872015
Lipid membranes as solvents for carbon nanoparticles
J Barnoud, G Rossi, L Monticelli
Physical Review Letters 112 (6), 068102, 2014
742014
Martini 3 coarse‐grained force field: small molecules
R Alessandri, J Barnoud, AS Gertsen, I Patmanidis, AH de Vries, ...
Advanced Theory and Simulations 5 (1), 2100391, 2022
722022
Hydrophobic compounds reshape membrane domains
J Barnoud, G Rossi, SJ Marrink, L Monticelli
PLoS Computational Biology 10 (10), e1003873, 2014
702014
Titratable Martini model for constant pH simulations
F Grünewald, PCT Souza, H Abdizadeh, J Barnoud, AH de Vries, ...
The Journal of chemical physics 153 (2), 2020
602020
Piezo1 forms specific, functionally important interactions with phosphoinositides and cholesterol
A Buyan, CD Cox, J Barnoud, J Li, HSM Chan, B Martinac, SJ Marrink, ...
Biophysical journal 119 (8), 1683-1697, 2020
552020
Proceedings of the 15th python in science conference
RJ Gowers, M Linke, J Barnoud, TJE Reddy, MN Melo, SL Seyler, ...
Austin, TX, 2016
502016
Interactive molecular dynamics in virtual reality is an effective tool for flexible substrate and inhibitor docking to the SARS-CoV-2 main protease
HM Deeks, RK Walters, J Barnoud, DR Glowacki, AJ Mulholland
Journal of chemical information and modeling 60 (12), 5803-5814, 2020
382020
PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
J Barnoud, H Santuz, P Craveur, AP Joseph, V Jallu, AG de Brevern, ...
PeerJ 5, e4013, 2017
352017
C60 fullerene promotes lung monolayer collapse
J Barnoud, L Urbini, L Monticelli
Journal of The Royal Society Interface 12 (104), 20140931, 2015
352015
Capturing choline–aromatics cation− π interactions in the MARTINI force field
HM Khan, PCT Souza, S Thallmair, J Barnoud, AH De Vries, SJ Marrink, ...
Journal of chemical theory and computation 16 (4), 2550-2560, 2020
342020
Resolving donor–acceptor interfaces and charge carrier energy levels of organic semiconductors with polar side chains
R Alessandri, S Sami, J Barnoud, AH de Vries, SJ Marrink, RWA Havenith
Advanced Functional Materials 30 (46), 2004799, 2020
332020
Alcohol interactions with lipid bilayers
T Kondela, J Gallová, T Hauß, J Barnoud, SJ Marrink, N Kučerka
Molecules 22 (12), 2078, 2017
332017
Coarse-grained force fields for molecular simulations
J Barnoud, L Monticelli
Molecular modeling of proteins, 125-149, 2015
332015
Sharing data from molecular simulations
M Abraham, R Apostolov, J Barnoud, P Bauer, C Blau, AMJJ Bonvin, ...
Journal of chemical information and modeling 59 (10), 4093-4099, 2019
292019
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