Publications

S. Parui, E. Brini, K. A. Dill. Computing Free Energies of Fold-Switching Proteins Using MELD x MD, Journal of Chemical Theory and Computation, 19, 6839 (2023). [link]

R. Nassar, E. Brini, S. Parui, C. Liu, G. Dignon, K. A. Dill, Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers,  Journal of Chemical Theory and Computation, Journal of Chemical Theory and Computation, 18, 1929 (2022) [link]

C. Liu, E. Brini, K. A. Dill, Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins, Journal of Chemical Theory and Computation, 18, 374 (2021) [link]

E. Brini, C. Simmerling, K. A. Dill, Protein storytelling through physics, Science, 370, eaaz3041 (2020) [link]

C. Liu, E. Brini, A. Perez, K. A. Dill, Computing ligand poses in proteins using MELD-accelerated MD, Journal of Chemical Theory and Computation, 16, 6377 (2020) [link]

D. Padhorny, K. A. Porter, M. Ignatov, A. Alekseenko, D. Beglov, S. Kotelnikov, R. Ashizawa, I. Desta, N. Alam, Z. Sun, E. Brini, K. A. Dill,O. Schueler Furman, S. Vajda, D.Kozakov, ClusPro in rounds 38-45 of CAPRI: Toward combining template-based methods with free docking, Proteins: Structure, Function, and Bioinformatics, 88, 1082 (2020) [link]

A. Khramushin, O. Marcu, N. Alam, O. Shimony, D. Padhorny, E. Brini, K. A. Dill, S. Vajda, D. Kozakov, O. Schueler-Furman, Modeling beta sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI Rounds 38-45, Proteins: Structure, Function, and Bioinformatics, 88, 1037 (2020) [link]

S. Kotelnikov, A. Alekseenko, C. Liu, M. Ignatov, D. Padhorny, E. Brini, M. Lukin, E. Coutsias, K. A. Dill, D. Kozakov, Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4, Journal of Computer-Aided Molecular Design, 34, 179 (2020) [link]

J. C. Robertson, R. Nassar, C. Liu, E. Brini, K. A. Dill, A. Perez, NMR-assisted protein structure prediction with MELDxMD, Proteins: Structure, Function, and Bioinformatics, 87, 1333 (2019) [link]

E. Brini, D. Kozakov, K. A. Dill, Predicting protein dimer structures using MELD x MD, Journal of Chemical Theory and Computation, 15, 3381 (2019) [link]

E. Brini, C. J. Fennell, M. Fernandez-Serra, B. Hribar-Lee, M. Lukšič, K. A. Dill, How water’s properties are encoded in its molecular structure and energies, Chemical Review, 117, 12385 (2017) [link]

A. Perez, J. A. Morrone, E. Brini, J. L. MacCallum, K. A. Dill, Blind protein structure prediction using accelerated free-energy simulations, Science Advances, 2, e1601274 (2016) [link]

E. Brini, S. S. Paranahewage, C. J. Fennell, K. A. Dill, Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules, Journal of Computer-Aided Molecular Design, 30, 1067 (2016) [link]

A. Perez, J. L. MacCallum, E. Brini, C. Simmerling, K. A. Dill, Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations, Journal of Chemical Theory and Computation, 11, 4770 (2015) [link]

E. Brini, E. A. Algaer, P. Ganguly, C. Li, F. Rodriguez-Ropero, N. F. van der Vegt, Systematic coarse- graining methods for soft matter simulations–a review, Soft Matter, 9, 2108 (2013) [link]

E. Brini, N. F. van der Vegt, Chemically transferable coarse-grained potentials from conditional reversible work calculations, The Journal of Chemical Physics, 137, 154113 (2012) [link]

F. Lugli, E. Brini, F. Zerbetto, Shape governs the motion of chemically propelled Janus swimmers, The Journal of Physical Chemistry C, 116, 592 (2012) [link]

E. Brini, C. R. Herbers, G. Deichmann, N. F. van der Vegt, Thermodynamic transferability of coarse-grained potentials for polymer–additive systems, Physical Chemistry Chemical Physics , 14, 11896 (2012) [link]

E. Brini, V. Marcon, N. F. van der Vegt, Conditional reversible work method for molecular coarse graining applications, Physical Chemistry Chemical Physics , 13, 10468 (2011) [link]

Link to Emiliano's Google Scholar