Lamoureux Laboratory

Preprints

S. Bhadra-Lobo, G. Derevyanko, G. Lamoureux. 2022. Dock2D: Synthetic data for the molecular recognition problem. arXiv:2212.03456. Link
G. Derevyanko, G. Lamoureux. 2019. Protein-protein docking using learned three-dimensional representations. bioRxiv. Link
G. Derevyanko, G. Lamoureux. 2018. TorchProteinLibrary: A computationally efficient, differentiable representation of protein structure. arXiv:1812.01108. Link

Articles

Google Scholar: Guillaume Lamoureux

(Articles cited more than 100 times are highlighted.)

T. N. Ozturk, D. E. Culham, L. Tempelhagen, J. M. Woods, G. Lamoureux. 2020. Salt-dependent Interactions Between the C-terminal Domain of Osmoregulatory Transporter ProP of Escherichia coli and the Lipid Membrane. J. Phys. Chem. B 124, 8209-8220. Link
C. Rupakheti, G. Lamoureux, A. D. MacKerell, Jr., B. Roux. 2020. Statistical Mechanics of Polarizable Force Fields Based on Classical Drude Oscillators With Dynamical Propagation by the Dual-Thermostat Extended Lagrangian. Journal of Chemical Physics 153, 114108. Link
E. A. Orabi, R. L. Davis, G. Lamoureux. 2020. Drude Polarizable Force Field for Cation-π Interactions of Alkali and Quaternary Ammonium Ions with Aromatic Amino Acid Side Chains. Journal of Computational Chemistry 41, 472-481. Link
B. Blessing, C. Trout, A. Morales, K. Rybacki, S. A. Love, G. Lamoureux, S. M. O'Malley, X. Hu, D. Salas-de la Cruz. 2020. The impact of composition and morphology on ionic conductivity of silk/cellulose bio-composites fabricated from ionic liquid and varying percentages of coagulation agents. International journal of molecular sciences 21, 4695. Link
L. Krohn, T. N. Ozturk, B. Vanderperre, B. Ouled Amar Bencheikh, J. A. Ruskey, S. B. Laurent, D. Spiegelman, R. B. Postuma, I. Arnulf, M. T. M. Hu, Y. Dauvilliers, B. Högl, A. Stefani, C. C. Monaca, G. Plazzi, E. Antelmi, L. Ferini-Strambi, A. Heidbreder, U. Rudakou, V. Cochen De Cock, P. Young, P. Wolf, P. Oliva, X. K. Zhang, L. Greenbaum, C. Liong, J.-F. Gagnon, A. Desautels, S. Hassin-Baer, J. Y. Montplaisir, N. Dupré, G. A. Rouleau, E. A. Fon, J.-F. Trempe, G. Lamoureux, R. N. Alcalay, Z. Gan-Or. 2019. Genetic, Structural, and Functional Evidence Link TMEM175 to Synucleinopathies Annals of Neurology 87, 139-153. Link
B. Blessing, C. Trout, A. Morales, K. Rybacki, S. A. Love, G. Lamoureux, S. M. O'Malley, X. Hu, D. Salas-de la Cruz. 2019. Morphology and ionic conductivity relationship in silk/cellulose biocomposites. Polymer International 68, 1580-1590. Link
D. E. Culham, D. Marom, R. Boutin, J. Garner, T. N. Ozturk, N. Sahtout, L. Tempelhagen, G. Lamoureux, J. M. Wood. 2018. Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP. Biophysical Journal 115, 2152-2166. Link
G. Derevyanko, S. Grudinin, Y. Bengio, G. Lamoureux. 2018. Deep convolutional networks for quality assessment of protein folds. Bioinformatics 34, 4046-4053. Link Preprint
E. A. Orabi, G. Lamoureux. 2018. Cation-π Interactions Between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. J. Phys. Chem. B 122, 2251-2260. Link
M. C. C. J. C. Ebert, J. G. Espinola, G. Lamoureux, J. N. Pelletier. 2017. Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations. ACS Catalysis 7, 6786-6797. Link
L. A. Carabet, M. Guertin, P. Lagüe, G. Lamoureux. 2017. Mechanism of the Nitric Oxide Dioxygenase Reaction of Mycobacterium tuberculosis Truncated Hemoglobin N. J. Phys. Chem. B 121, 8706-8718. Link
M. C. C. J. C. Ebert, S. L. Dürr, A. A. Houle, G. Lamoureux, J. N. Pelletier. 2016. Evolution of P450 Monooxygenases toward Formation of Transient Channels and Exclusion of Nonproductive Gases. ACS Catalysis 6, 7426-7437. Link
A. P. Ramos, P. Lagüe, G. Lamoureux, M. Lafleur. 2016. Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining 2H NMR Spectroscopy and Molecular Dynamics Simulations. J. Phys. Chem. B 120, 6951-6960. Link
S. Moreira, E. Noutahi, G. Lamoureux, G. Burger. 2015. Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2. BMC Structural Biology 15, 20. Link
S. Baday, E. A. Orabi, S. Wang, G. Lamoureux, S. Bernèche. 2015. Mechanism of NH4+ recruitment and NH3 transport in Rh proteins. Structure 23, 1550-1557. Link
J.-F. Rhéault, E. Gagné, M. Guertin, G. Lamoureux, M. Auger, P. Lagüe. 2015. Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study. Biochemistry 54, 2073-2084. Link
O. Fürst, C. Nichols, G. Lamoureux, N. D'Avanzo. 2014. Identification of a Cholesterol Binding Pocket in Inward Rectifier K+ (Kir) Channels. Biophys. J. 107, 2786-2796. Link
Q. Yu, E. M. Rodriguez, R. Naccache, P. Forgione, G. Lamoureux, F. Sanz-Rodriguez, D. Scheglmann, and John A. Capobianco. 2014. Chemical Modification of Temoporfin - A Second Generation Photosensitizer Activated Using Upconverting Nanoparticles for Singlet Oxygen Generation. Chem. Commun. 50, 12150-12153. Link
E. A. Orabi and G. Lamoureux. 2014. Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid. J. Chem. Theory Comput. 10, 3221-3235. Link
S. Wang, L. MacKay, and G. Lamoureux. 2014. Development of Semiempirical Models for Proton Transfer Reactions in Water. J. Chem. Theory Comput. 10, 2881-2890. Link
S. Baday, S. Wang, G. Lamoureux, and S. Bernèche. 2013. Different Hydration Patterns in the Pores of AmtB and RhCG Could Determine Their Transport Mechanisms. Biochemistry 52, 7091-7098. Link
E. A. Orabi and G. Lamoureux. 2013. Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia. J. Chem. Theory Comput. 9, 2324-2338. Link
E. A. Orabi and G. Lamoureux. 2013. Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia. J. Chem. Theory Comput. 9, 2035-2051. Link
G. Lamoureux and E. A. Orabi. 2012. Molecular modeling of cation-π interactions. Molecular Simulation 38, 704-722 (Invited article, "New Developments in Molecular Simulation") Link
S. Wang, E. A. Orabi, S. Baday, S. Bernèche, and G. Lamoureux. 2012. Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate. J. Am. Chem. Soc. USA 134, 10419-10427. Link
E. A. Orabi and G. Lamoureux. 2012. Cation-π and π-π Interactions in Aqueous Solution Studied Using Polarizable Potential Models. J. Chem. Theory Comput. 8, 182-193. Link
G. Lamoureux, A. Javelle, S. Baday, S. Wang, and S. Bernèche. 2010. Transport mechanisms in the ammonium transporter family. Transf. Clin. Biol. 17, 168-175. Link
H. Yu, T. W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov, V. M. Anisimov, A. D. MacKerell, Jr., and B. Roux. 2010. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J. Chem. Theory Comput. 6, 774-786. Link
P. E. M. Lopes, G. Lamoureux, and A. D. Mackerell, Jr. 2009. Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J. Comput. Chem. 30, 1821-1838. Link
G. Lamoureux, J. D. Faraldo-Gómez, S. Krupin, and S. Yu. Noskov. 2009. Polarizable model of chloroform based on classical Drude oscillators. Chem. Phys. Lett. 468, 270-274. Link
J. Blumberger and G. Lamoureux. 2008. Reorganization free energies and quantum corrections for a model electron self-exchange reaction: comparison of polarizable and non-polarizable solvent models. Mol. Phys. 106, 1597-1611. (Invited article, "Special Issue in Honour of Professor Anthony J. Stone") Link
T. W. Whitfield, S. Varma, E. Harder, G. Lamoureux, S. B. Rempe, and B. Roux. 2007. Theoretical study of aqueous solvation of K+ comparing ab initio, polarizable, and fixed-charge models. J. Chem. Theory Comput. 3, 2068-2082. (Invited article, "Special Issue on Polarization") Link
J. Blumberger,* G. Lamoureux,* and M. L. Klein. 2007. Peptide hydrolysis in thermolysin: Ab initio QM/MM investigation of the Glu143-assisted water addition mechanism. J. Chem. Theory Comput. 3, 1837-1850. Link
G. Lamoureux, M. L. Klein, and S. Bernèche. 2007. A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophys. J. 92, L82-L84. Link
P. E. M. Lopes, G. Lamoureux, B. Roux, and A. D. MacKerell, Jr. 2007. Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator. J. Phys. Chem. B 111, 2873-2885. Link
M. Dal Peraro, K. Spiegel, G. Lamoureux, M. De Vivo, W. F. DeGrado, and M. L. Klein. 2007. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J. Struct. Biol. 157, 444-453. (Invited article, "Special Issue: Advances in Molecular Dynamics Simulations") Link
G. Lamoureux and B. Roux. 2006. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J. Phys. Chem. B 110, 3308-3322. Link
G. Lamoureux, E. Harder, I. V. Vorobyov, B. Roux, and A. D. MacKerell, Jr. 2006. A polarizable model of water for molecular dynamics simulations of biomolecules. Chem. Phys. Lett. 418, 245-249. Link
V. M. Anisimov, G. Lamoureux, I. V. Vorobyov, N. Huang, B. Roux, and A. D. MacKerell, Jr. 2005. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. J. Chem. Theory Comput. 1, 153-168. Link
S. Yu. Noskov,* G. Lamoureux,* and B. Roux. 2005. Molecular Dynamics Study of Hydration in Ethanol-Water Mixtures Using a Polarizable Force Field. J. Phys. Chem. B 109, 6705-6713. (Invited article, "David Chandler Festschrift") Link
G. Lamoureux, A. D. MacKerell, Jr., and B. Roux. 2003. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 119, 5185-5197. Link
G. Lamoureux and B. Roux. 2003. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm. J. Chem. Phys. 119, 3025-3039. Link
G. Lamoureux, A. Caillé, and D. Sénéchal. 1998. Thermal phase diagrams of columnar liquid crystals. Phys. Rev. E 58, 5898-5908. Link

Recent invited talks

End-to-end learning of biomolecular interactions, CECAM Workshop: Progress and developments of Artificial Intelligence for Drug Design (Genoa, Italy, June 2019)
Learning protein structure and function, McGill University, Physics & AI Workshop (Montreal, QC, May 2019)
End-to-end learning of protein structure and function, Computer-Aided Drug Design Center, University of Maryland School of Pharmacy (Baltimore, MD, April 2019)
Learning protein structure and function, CILVR Lab, NYU Center for Data Science (New York, NY, November 2018)
Modeling and prediction of protein structure using deep neural networks, American Chemical Society 256th National Meeting (Boston, MA, August 2018)
Deep Learning for Protein Structure Prediction and Protein Folding, World Congress in Computational Mechanics (New York, NY, July 2018)
Molecular dynamics simulations of membrane proteins, GEPROM Workshop: From Genetics to Medicine (Montréal, QC, June 2018)
Deep Neural Networks for Protein Structure Prediction and Protein Folding, 101th Canadian Chemistry Conference and Exhibition (Edmonton, AB, May 2018)
Molecular modeling of protein structure and function, Department of Chemistry, Rutgers University – Camden (Camden, NJ, February 2017)
Using Deep Learning to Predict Residue Contacts in Proteins, 99th Canadian Chemistry Conference and Exhibition (Halifax, NS, June 2016)
Approches "deep learning" pour la prédiction de structures de protéines, Département de biochimie, Université de Sherbrooke (Sherbrooke, QC, June 2016)
Molecular modeling of ammonium transport in ammonium transport in proteins of the Amt/Rh family, Department of Biochemistry, University of Toronto (Toronto, ON, April 2016)
Molecular modeling of proton-coupled transport in membrane proteins, Department of Chemistry, Dalhousie University (Halifax, NS, July 2015)
The Nitric Oxide Dioxygenase Reaction in Truncated Hemoglobin N of Mycobacterium Tuberculosis, CECAM Workshop: Modeling activity versus selectivity in metalloproteins (Paris, France, June 2015)
Semiempirical Models for Proton Transfer Reactions in Solution, 98th Canadian Chemistry Conference and Exhibition (Ottawa, ON, June 2015)
Modélisation moléculaire du mécanisme des transporteurs d'ammonium de la famille Amt/Rh, Département de biochimie, Université de Sherbrooke (Sherbrooke, QC, May 2015)
Molecular modeling of proton-coupled transport in membrane proteins, Schrödinger (New York, NY, February 2015)
Molecular modeling of proton-coupled transport in membrane proteins, Department of Chemistry, CUNY Staten Island (New York, NY, February 2015)