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Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field
Astrid F Brandner
,
Iain P S Smith
,
Siewert J Marrink
,
Paulo C T Souza
,
Syma Khalid
Article dans une revue
hal-04896377
v1
|
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Bending of a lipid membrane edge by annexin A5 trimers
Mayank Prakash Pandey
,
Paulo C. T. Souza
,
Weria Pezeshkian
,
Himanshu Khandelia
Article dans une revue
hal-04745112
v1
|
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Assessing the Martini 3 protein model: A review of its path and potential
Luís Borges-Araújo
,
Gilberto P Pereira
,
Mariana Valério
,
Paulo C. T. Souza
Article dans une revue
hal-04745091
v1
|
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Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7
Simone Albani
,
Vishal Sudha Bhagavath Eswaran
,
Alessia Piergentili
,
Paulo C. T. Souza
,
Angelika Lampert
et al.
Article dans une revue
hal-04745121
v1
|
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Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics
Gilberto P Pereira
,
Riccardo Alessandri
,
Moisés Domínguez
,
Rocío Araya-Osorio
,
Linus Grünewald
et al.
Article dans une revue
hal-04745117
v1
|
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Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex
Yeonji Chung
,
Chewon Yim
,
Gilberto Pereira
,
Sungjoon Son
,
Lisbeth Kjølbye
et al.
Article dans une revue
hal-04896361
v1
|
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OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field
Kasper B Pedersen
,
Luís Borges-Araújo
,
Amanda D Stange
,
Paulo C. T. Souza
,
Siewert-Jan Marrink
et al.
Article dans une revue
hal-04745097
v1
|
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A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1
Alessio Bartocci
,
Andrea Grazzi
,
Nour Awad
,
Pierre-Jean Corringer
,
Paulo C. T. Souza
et al.
Article dans une revue
hal-04745126
v1
|
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Martini 3 Coarse-Grained Force Field for Cholesterol
Luís Borges-Araújo
,
Ana C Borges-Araújo
,
Tugba Nur Ozturk
,
Daniel P Ramirez-Echemendia
,
Balázs Fábián
et al.
Article dans une revue
hal-04296756
v1
|
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Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG
Charly Empereur-Mot
,
Kasper B Pedersen
,
Riccardo Capelli
,
Martina Crippa
,
Cristina Caruso
et al.
Article dans une revue
hal-04296720
v1
|
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Pragmatic Coarse-Graining of Proteins: Models and Applications
Luís Borges-Araújo
,
Ilias Patmanidis
,
Akhil Singh
,
Lucianna Santos
,
Adam Sieradzan
et al.
Article dans une revue
(article de synthèse)
hal-04296801
v1
|
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Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking
Gilberto P Pereira
,
Brian Jiménez-García
,
Riccardo Pellarin
,
Guillaume Launay
,
Sangwook Wu
et al.
Article dans une revue
hal-04274715
v1
|
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Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
Panagiotis Koukos
,
Sepehr Dehghani-Ghahnaviyeh
,
Camilo Velez-Vega
,
John Manchester
,
D. Peter Tieleman
et al.
Article dans une revue
hal-04745158
v1
|
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Expulsion mechanism of the substrate-translocating subunit in ECF transporters
Chancievan Thangaratnarajah
,
Mark Nijland
,
Luís Borges-Araújo
,
Aike Jeucken
,
Jan Rheinberger
et al.
Article dans une revue
hal-04296762
v1
|
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Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
Eleonora Diamanti
,
Paulo Cesar Telles de Souza
,
Inda Setyawati
,
Spyridon Bousis
,
Leticia M Gómez
et al.
Article dans une revue
hal-04296925
v1
|
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Two decades of Martini: Better beads, broader scope
Siewert Marrink
,
Luca Monticelli
,
Manuel Melo
,
Riccardo Alessandri
,
D. Peter Tieleman
et al.
Article dans une revue
hal-03864638
v1
|
|
Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials
Fabian Grünewald
,
Riccardo Alessandri
,
Peter C Kroon
,
Luca Monticelli
,
Paulo C T Souza
et al.
Article dans une revue
hal-03855658
v1
|
|
Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes
Neila Machado
,
Bart Bruininks
,
Priyanka Singh
,
Laurita dos Santos
,
Carine Dal Pizzol
et al.
Article dans une revue
hal-03863122
v1
|
|
Towards design of drugs and delivery systems with the Martini coarse-grained model
Lisbeth Kjølbye
,
Gilberto Pereira
,
Alessio Bartocci
,
Martina Pannuzzo
,
Simone Albani
et al.
Article dans une revue
hal-03864646
v1
|
|
Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field
Luís Borges-Araújo
,
Paulo Souza
,
Fábio Fernandes
,
Manuel Melo
Article dans une revue
hal-03864628
v1
|
|
Modelling structural properties of cyanine dye nanotubes at coarse-grained level
Ilias Patmanidis
,
Paulo Souza
,
Selim Sami
,
Remco Havenith
,
Alex de Vries
et al.
Article dans une revue
hal-03864633
v1
|
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Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins
Shengli Zhang
,
Gang Huang
,
Roderick Corstiaan Abraham Versloot
,
Bart Marlon Herwig Bruininks
,
Paulo Cesar Telles de Souza
et al.
Article dans une revue
hal-03863245
v1
|
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Martini 3: a general purpose force field for coarse-grained molecular dynamics
Paulo Souza
,
Riccardo Alessandri
,
Jonathan Barnoud
,
Sebastian Thallmair
,
Ignacio Faustino
et al.
Article dans une revue
hal-03863208
v1
|
|
Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies
Bart Bruininks
,
Albert Thie
,
Paulo Souza
,
Tsjerk Wassenaar
,
Shirin Faraji
et al.
Article dans une revue
hal-03863224
v1
|
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Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model
Maria Tsanai
,
Pim W. Frederix
,
Carsten Schroer
,
Paulo Souza
,
Siewert Marrink
Article dans une revue
hal-03863190
v1
|
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Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties
Petteri Vainikka
,
Sebastian Thallmair
,
Paulo Cesar Telles Souza
,
Siewert Marrink
Article dans une revue
hal-03864619
v1
|
|
Titratable Martini model for constant pH simulations
Fabian Grünewald
,
Paulo C. T. Souza
,
Haleh Abdizadeh
,
Jonathan Barnoud
,
Alex de Vries
et al.
Article dans une revue
hal-04296865
v1
|
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Protein–ligand binding with the coarse-grained Martini model
Paulo C T Souza
,
Sebastian Thallmair
,
Paolo Conflitti
,
Carlos Ramírez-Palacios
,
Riccardo Alessandri
et al.
Article dans une revue
hal-04296809
v1
|
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Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction
Luis Itza Vazquez-Salazar
,
Michele Selle
,
Alex H de Vries
,
Siewert J Marrink
,
Paulo C T Souza
Article dans une revue
hal-04296861
v1
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