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 Laboratory (LANL), Los Alamos, NM (United States), 2019 | 1186 | 2019 |
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 | 693 | 2021 |
Polystyrene nanoparticles perturb lipid membranes G Rossi, J Barnoud, L Monticelli The journal of physical chemistry letters 5 (1), 241-246, 2014 | 347 | 2014 |
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 | 138 | 2013 |
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 | 124 | 2012 |
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 | 89 | 2015 |
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 | 86 | 2022 |
Hydrophobic compounds reshape membrane domains J Barnoud, G Rossi, SJ Marrink, L Monticelli PLoS Computational Biology 10 (10), e1003873, 2014 | 78 | 2014 |
Lipid membranes as solvents for carbon nanoparticles J Barnoud, G Rossi, L Monticelli Physical Review Letters 112 (6), 068102, 2014 | 77 | 2014 |
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 | 64 | 2020 |
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 | 64 | 2020 |
Proceedings of the 15th python in science conference RJ Gowers, M Linke, J Barnoud, TJE Reddy, MN Melo, SL Seyler, ... Austin, TX, 2016 | 59 | 2016 |
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 | 42 | 2020 |
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 | 41 | 2020 |
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 | 37 | 2017 |
Martinize2 and vermouth: Unified framework for topology generation PC Kroon, F Grünewald, J Barnoud, M van Tilburg, PCT Souza, ... arXiv preprint arXiv:2212.01191, 2022 | 35 | 2022 |
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 | 35 | 2019 |
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 | 34 | 2020 |
Alcohol interactions with lipid bilayers T Kondela, J Gallová, T Hauß, J Barnoud, SJ Marrink, N Kučerka Molecules 22 (12), 2078, 2017 | 34 | 2017 |
C60 fullerene promotes lung monolayer collapse J Barnoud, L Urbini, L Monticelli Journal of The Royal Society Interface 12 (104), 20140931, 2015 | 34 | 2015 |