| CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, ... Journal of computational chemistry 31 (4), 671-690, 2010 | 6207 | 2010 |
| Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles RB Best, X Zhu, J Shim, PEM Lopes, J Mittal, M Feig, AD MacKerell Jr Journal of chemical theory and computation 8 (9), 3257-3273, 2012 | 4044 | 2012 |
| Polarizable force field for peptides and proteins based on the classical drude oscillator PEM Lopes, J Huang, J Shim, Y Luo, H Li, B Roux, AD MacKerell Jr Journal of chemical theory and computation 9 (12), 5430-5449, 2013 | 409 | 2013 |
| Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications PEM Lopes, B Roux, AD MacKerell Theoretical Chemistry Accounts 124, 11-28, 2009 | 390 | 2009 |
| Development of an empirical force field for silica. Application to the quartz− water interface PEM Lopes, V Murashov, M Tazi, E Demchuk, AD MacKerell The Journal of Physical Chemistry B 110 (6), 2782-2792, 2006 | 270 | 2006 |
| Recent developments and applications of the CHARMM force fields X Zhu, PEM Lopes, AD MacKerell Jr Wiley Interdisciplinary Reviews: Computational Molecular Science 2 (1), 167-185, 2012 | 239 | 2012 |
| Current status of protein force fields for molecular dynamics simulations PEM Lopes, O Guvench, AD MacKerell Molecular modeling of proteins, 47-71, 2015 | 230 | 2015 |
| Polarizable empirical force field for aromatic compounds based on the classical drude oscillator PEM Lopes, G Lamoureux, B Roux, AD MacKerell The Journal of Physical Chemistry B 111 (11), 2873-2885, 2007 | 194 | 2007 |
| A polarizable force field of dipalmitoylphosphatidylcholine based on the classical drude model for molecular dynamics simulations of lipids J Chowdhary, E Harder, PEM Lopes, L Huang, AD MacKerell Jr, B Roux The Journal of Physical Chemistry B 117 (31), 9142-9160, 2013 | 176 | 2013 |
| Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator E Harder, VM Anisimov, IV Vorobyov, PEM Lopes, SY Noskov, ... Journal of chemical theory and computation 2 (6), 1587-1597, 2006 | 175 | 2006 |
| Accurate calculation of hydration free energies using pair-specific Lennard-Jones parameters in the CHARMM Drude polarizable force field CM Baker, PEM Lopes, X Zhu, B Roux, AD MacKerell Jr Journal of chemical theory and computation 6 (4), 1181-1198, 2010 | 159 | 2010 |
| Recent advances in polarizable force fields for macromolecules: microsecond simulations of proteins using the classical Drude oscillator model J Huang, PEM Lopes, B Roux, AD MacKerell Jr The journal of physical chemistry letters 5 (18), 3144-3150, 2014 | 150 | 2014 |
| Six-site polarizable model of water based on the classical Drude oscillator W Yu, PEM Lopes, B Roux, AD MacKerell The Journal of chemical physics 138 (3), 2013 | 131 | 2013 |
| Polarizable empirical force field for nitrogen‐containing heteroaromatic compounds based on the classical Drude oscillator PEM Lopes, G Lamoureux, AD Mackerell Jr Journal of computational chemistry 30 (12), 1821-1838, 2009 | 81 | 2009 |
| The small molecule IMR-1 inhibits the notch transcriptional activation complex to suppress tumorigenesis L Astudillo, TG Da Silva, Z Wang, X Han, K Jin, J VanWye, X Zhu, ... Cancer research 76 (12), 3593-3603, 2016 | 70 | 2016 |
| MacKerell Jr AD J Huang, PEM Lopes, B Roux Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond …, 2014 | 65 | 2014 |
| Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: novel antimicrobial targets LM Furci, P Lopes, S Eakanunkul, S Zhong, AD MacKerell, A Wilks Journal of medicinal chemistry 50 (16), 3804-3813, 2007 | 65 | 2007 |
| Polarizable empirical force field for acyclic polyalcohols based on the classical drude oscillator X He, PEM Lopes, AD MacKerell Jr Biopolymers 99 (10), 724-738, 2013 | 58 | 2013 |
| Polarizable force field for molecular ions based on the classical Drude oscillator FY Lin, PEM Lopes, E Harder, B Roux, AD MacKerell Jr Journal of chemical information and modeling 58 (5), 993-1004, 2018 | 56 | 2018 |
| Holo-Ni(II)HpNikR Is an Asymmetric Tetramer Containing Two Different Nickel-Binding Sites AL West, F St. John, PEM Lopes, AD MacKerell Jr, E Pozharski, ... Journal of the American Chemical Society 132 (41), 14447-14456, 2010 | 40 | 2010 |
