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This folder holds the following references to publications, sorted by year and author.

There are 27 references in this bibliography folder.

Bongiovanni, TR, Latario, CJ, Le Cras, Y, Trus, E, Robitaille, S, Swartz, K, Schmidtke, D, Vincent, M, Kosta, A, Orth, J, Stengel, F, Pellarin, R, Rocha, EPC, Ross, BD, and Durand, E (2024).
Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota.
Nat Commun, 15(1):429.

Martin, J (2024).
AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility
Journal of Chemical Information and Modeling.

Sabei, A, Hognon, C, Martin, J, and Frezza, E (2024).
Dynamics of Protein–RNA Interfaces Using All-Atom Molecular Dynamics Simulations
The Journal of Physical Chemistry B, 128(20):4865–4886.

Afonine, PV, Gobet, A, Moissonnier, L, Martin, J, Poon, BK, and Chaptal, V (2023).
Conformational space exploration of cryo-EM structures by variability refinement.
Biochim Biophys Acta Biomembr, 1865(4):184133.

Alessandri, R, Thallmair, S, Herrero, CG, Mera-Adasme, R, Marrink, SJ, and Souza, PCT (2023).
A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations
In: A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, chap. 1, AIP Publishing LLC. (ISBN: 978-0-7354-2524-8).

Borges-Araújo, L, Borges-Araújo, AC, Ozturk, TN, Ramirez-Echemendia, DP, Fábián, B, Carpenter, TS, Thallmair, S, Barnoud, J, Ingólfsson, HI, Hummer, G, Tieleman, DP, Marrink, SJ, Souza, PCT, and Melo, MN (2023).
Martini 3 Coarse-Grained Force Field for Cholesterol
Journal of Chemical Theory and Computation, 19(20):7387-7404.

Borges-Araújo, L, Patmanidis, I, Singh, AP, Santos, LHS, Sieradzan, AK, Vanni, S, Czaplewski, C, Pantano, S, Shinoda, W, Monticelli, L, Liwo, A, Marrink, SJ, and Souza, PCT (2023).
Pragmatic Coarse-Graining of Proteins: Models and Applications
Journal of Chemical Theory and Computation, 19(20):7112-7135.

Diamanti, E, Souza, PCT, Setyawati, I, Bousis, S, Gómez, LM, Swier, LJ, Shams, A, Tsarenko, A, Stanek, WK, Jäger, M, and others (2023).
Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
Communications biology, 6(1):1182.

Empereur-mot, C, Pedersen, KB, Capelli, R, Crippa, M, Caruso, C, Perrone, M, Souza, PCT, Marrink, SJ, and Pavan, GM (2023).
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG
Journal of Chemical Information and Modeling, 63(12):3827-3838.

Hilpert, C, Beranger, L, Souza, PCT, Vainikka, PA, Nieto, V, Marrink, SJ, Monticelli, L, and Launay, G (2023).
Facilitating CG Simulations with MAD: The MArtini Database Server
Journal of Chemical Information and Modeling, 63(3):702-710.

Ingólfsson, HI, Rizuan, A, Liu, X, Mohanty, P, Souza, PC, Marrink, SJ, Bowers, MT, Mittal, J, and Berry, J (2023).
Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation
Biophysical Journal, 122(22):4370-4381.

Kandolo, O, Cherrak, Y, Filella-Merce, I, Le Guenno, H, Kosta, A, Espinosa, L, Santucci, P, Verthuy, C, Lebrun, R, Nilges, M, Pellarin, R, and Durand, E (2023).
Acinetobacter type VI secretion system comprises a non-canonical membrane complex.
PLoS Pathog, 19(9):e1011687.

Koukos, PI, Dehghani-Ghahnaviyeh, S, Velez-Vega, C, Manchester, J, Tieleman, DP, Duca, JS, Souza, PCT, and Cournia, Z (2023).
Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
Journal of Chemical Theory and Computation, 19(23):8901-8918.

MacCallum, JL, Hu, S, Lenz, S, Souza, PC, Corradi, V, and Tieleman, DP (2023).
An implementation of the Martini coarse-grained force field in OpenMM
Biophysical Journal, 122(14):2864–2870.

Marrink, SJ, Monticelli, L, Melo, MN, Alessandri, R, Tieleman, DP, and Souza, PCT (2023).
Two decades of Martini: Better beads, broader scope
WIREs Computational Molecular Science, 13(1):e1620.

Martin, J, Robert, X, Gouet, P, Falson, P, and Chaptal, V (2023).
Specific Xray diffraction patterns of membrane proteins caused by secondary structure collinearity.
Biochim Biophys Acta Biomembr, 1865(1):184065.

Pereira, GP, Jiménez-García, B, Pellarin, R, Launay, G, Wu, S, Martin, J, and Souza, PCT (2023).
Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking.
J Chem Inf Model, 63(21):6823-6833.

Sabei, A, Caldas Baia, TG, Saffar, R, Martin, J, and Frezza, E (2023).
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes.
J Chem Inf Model, 63(8):2554-2572.

Sahoo, AR, Souza, PC, Meng, Z, and Buck, M (2023).
Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer
Structure, 31(6):735–745.e2.

Sami, S, Grünewald, F, Souza, PCT, and Marrink, SJ (2023).
A Guide to Titratable Martini Simulations
In: A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, chap. 4, AIP Publishing LLC. (ISBN: 978-0-7354-2524-8).

Schweke, H, Xu, Q, Tauriello, G, Pantolini, L, Schwede, T, Cazals, F, Lhéritier, A, Fernandez-Recio, J, Rodríguez-Lumbreras, L�, Schueler-Furman, O, and others (2023).
Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study

Stroh, KS, Souza, PCT, Monticelli, L, and Risselada, HJ (2023).
CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization
Journal of Chemical Theory and Computation, 19(22):8384-8400.

Thangaratnarajah, C, Nijland, M, Borges-Araújo, L, Jeucken, A, Rheinberger, J, Marrink, SJ, Souza, PCT, Paulino, C, and Slotboom, DJ (2023).
Expulsion mechanism of the substrate-translocating subunit in ECF transporters
Nature Communications, 14(1).

Vanlioğlu, E, Santin, YG, Filella-Merce, I, Pellarin, R, and Cascales, E (2023).
Coevolution-Guided Mapping of the Type VI Secretion Membrane Complex-Baseplate Interface.
J Mol Biol, 435(2):167918.

Waclawiková, B, Souza, PCT, Schwalbe, M, Neochoritis, CG, Hoornenborg, W, Nelemans, SA, Marrink, SJ, and El Aidy, S (2023).
Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats
Gut Microbes, 15(1):2154544.

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