| CHARMM: the biomolecular simulation program BR Brooks, CL Brooks III, AD Mackerell Jr, L Nilsson, RJ Petrella, B Roux, ... Journal of computational chemistry 30 (10), 1545-1614, 2009 | 8734 | 2009 |
| Free energy simulations come of age: Protein− ligand recognition T Simonson, G Archontis, M Karplus Accounts of chemical research 35 (6), 430-437, 2002 | 454 | 2002 |
| Self-assembly of phenylalanine oligopeptides: insights from experiments and simulations P Tamamis, L Adler-Abramovich, M Reches, K Marshall, P Sikorski, ... Biophysical journal 96 (12), 5020-5029, 2009 | 255 | 2009 |
| Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics T Lazaridis, G Archontis, M Karplus Advances in protein chemistry 47, 231-306, 1995 | 235 | 1995 |
| MM-GB (PB) SA calculations of protein-ligand binding free energies JM Hayes, G Archontis Molecular dynamics-studies of synthetic and biological macromolecules, 171-190, 2012 | 153 | 2012 |
| Free energy simulations: the meaning of the individual contributions from a component analysis S Boresch, G Archontis, M Karplus Proteins: Structure, Function, and Bioinformatics 20 (1), 25-33, 1994 | 151 | 1994 |
| Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein− Ligand Binding. T Simonson, G Archontis, M Karplus The Journal of Physical Chemistry B 101 (41), 8349-8362, 1997 | 136 | 1997 |
| Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase G Archontis, T Simonson, M Karplus Journal of molecular biology 306 (2), 307-327, 2001 | 134 | 2001 |
| Karplus M. CHARMM: the biomolecular simulation program BR Brooks, CL Brooks III, AD Mackerell, L Nilsson, RJ Petrella, B Roux, ... J. Comput. Chem 30, 1545-1614, 2009 | 114* | 2009 |
| Kinetics, in silico docking, molecular dynamics, and MM‐GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP … JM Hayes, VT Skamnaki, G Archontis, C Lamprakis, J Sarrou, N Bischler, ... Proteins: Structure, Function, and Bioinformatics 79 (3), 703-719, 2011 | 108 | 2011 |
| A Poisson− Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation T Simonson, G Archontis, M Karplus The Journal of Physical Chemistry B 103 (29), 6142-6156, 1999 | 104 | 1999 |
| Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitors M Benltifa, JM Hayes, S Vidal, D Gueyrard, PG Goekjian, JP Praly, ... Bioorganic & medicinal chemistry 17 (20), 7368-7380, 2009 | 100 | 2009 |
| Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis J Van Heemst, DTSL Jansen, S Polydorides, AK Moustakas, M Bax, ... Nature communications 6 (1), 6681, 2015 | 91 | 2015 |
| Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations G Archontis, T Simonson, D Moras, M Karplus Journal of molecular biology 275 (5), 823-846, 1998 | 83 | 1998 |
| Attraction of iodide ions by the free water surface, revealed by simulations with a polarizable force field based on Drude oscillators G Archontis, E Leontidis, G Andreou The Journal of Physical Chemistry B 109 (38), 17957-17966, 2005 | 79 | 2005 |
| Proton binding to proteins: a free-energy component analysis using a dielectric continuum model G Archontis, T Simonson Biophysical journal 88 (6), 3888-3904, 2005 | 79 | 2005 |
| Computational sidechain placement and protein mutagenesis with implicit solvent models A Lopes, A Alexandrov, C Bathelt, G Archontis, T Simonson Proteins: Structure, Function, and Bioinformatics 67 (4), 853-867, 2007 | 73 | 2007 |
| Toward rational design of selective molecularly imprinted polymers (MIPs) for proteins: computational and experimental studies of acrylamide based polymers for myoglobin MV Sullivan, SR Dennison, G Archontis, SM Reddy, JM Hayes The Journal of Physical Chemistry B 123 (26), 5432-5443, 2019 | 66 | 2019 |
| Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model G Archontis, T Simonson Journal of the American Chemical Society 123 (44), 11047-11056, 2001 | 57 | 2001 |
| X., Yang, W., York BR Brooks III, ADM CLB Jr, L Nilsson, RJ Petrella, B Roux, Y Won, ... IPSJ SIG Technical Report DM and Karplus, M.: CHARMM: the biomolecular …, 2009 | 52 | 2009 |
