Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD W Jiang, JC Phillips, L Huang, M Fajer, Y Meng, JC Gumbart, Y Luo, ... Computer physics communications 185 (3), 908-916, 2014 | 132 | 2014 |

Simulated scaling method for localized enhanced sampling and simultaneous “alchemical” free energy simulations: A general method for molecular mechanical, quantum mechanical … H Li, M Fajer, W Yang The Journal of chemical physics 126 (2), 2007 | 102 | 2007 |

Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration M Fajer, D Hamelberg, JA McCammon Journal of chemical theory and computation 4 (10), 1565-1569, 2008 | 101 | 2008 |

Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method MI Fajer, H Li, W Yang, PG Fajer Journal of the American Chemical Society 129 (45), 13840-13846, 2007 | 51 | 2007 |

The activation of c-Src tyrosine kinase: conformational transition pathway and free energy landscape M Fajer, Y Meng, B Roux The Journal of Physical Chemistry B 121 (15), 3352-3363, 2017 | 50 | 2017 |

w-REXAMD: A Hamiltonian replica exchange approach to improve free energy calculations for systems with kinetically trapped conformations M Arrar, CAF de Oliveira, M Fajer, W Sinko, JA McCammon Journal of chemical theory and computation 9 (1), 18-23, 2013 | 46 | 2013 |

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics M Fajer, RV Swift, JA McCammon Journal of computational chemistry 30 (11), 1719-1725, 2009 | 42 | 2009 |

On the role of dewetting transitions in host–guest binding free energy calculations KE Rogers, JM Ortiz-Sánchez, R Baron, M Fajer, CAF de Oliveira, ... Journal of chemical theory and computation 9 (1), 46-53, 2013 | 31 | 2013 |

Computational study of non-conductive selectivity filter conformations and C-type inactivation in a voltage-dependent potassium channel J Li, R Shen, A Rohaim, R Mendoza Uriarte, M Fajer, E Perozo, B Roux Journal of General Physiology 153 (9), e202112875, 2021 | 14 | 2021 |

Full atom simulations of spin label conformations P Fajer, M Fajer, M Zawrotny, W Yang Methods in enzymology 563, 623-642, 2015 | 12 | 2015 |

Molecular modeling of spin labels M Fajer, PG Fajer, KL Sale ESR spectroscopy in membrane biophysics. Springer, New York, 253-259, 2007 | 8 | 2007 |

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering O Gerlits, M Fajer, X Cheng, DK Blumenthal, Z Radić, A Kovalevsky Structure 30 (11), 1538-1549. e3, 2022 | 7 | 2022 |

Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects DK Blumenthal, X Cheng, M Fajer, KY Ho, J Rohrer, O Gerlits, P Taylor, ... Journal of Biological Chemistry 297 (3), 2021 | 7 | 2021 |

Intrinsic free energy of the conformational transition of the KcsA signature peptide from conducting to nonconducting state IV Khavrutskii, M Fajer, JA McCammon Journal of chemical theory and computation 4 (9), 1541-1554, 2008 | 7 | 2008 |

Quantitatively Accounting for Protein Reorganization in Computer-Aided Drug Design M Fajer, K Borrelli, R Abel, L Wang Journal of Chemical Theory and Computation, 2023 | 4 | 2023 |

Generalized ensemble sampling of enzyme reaction free energy pathways D Wu, MI Fajer, L Cao, X Cheng, W Yang Methods in enzymology 577, 57-74, 2016 | 3 | 2016 |

Simulation of spin label structure and its implication in molecular characterization P Fajer, M Fajer, M Zawrotny, W Yang Methods in enzymology 563, 623, 2015 | 3 | 2015 |

Crystallographic studies of human acetylcholinesterase reactivation by oximes: Towards a neutron structure O Gerlits, M Fajer, X Cheng, D Blumenthal, P Taylor, Z Radic, ... The FASEB Journal 30, 1191.1-1191.1, 2016 | 1 | 2016 |

Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD W Jiang, J Phillips, L Huang, M Fajer, Y Meng, JC Gumbart, K Schulten Biophysical Journal 106 (2), 412a, 2014 | 1 | 2014 |

ROOM-TEMPERATURE CRYSTALLOGRAPHY AND NEUTRON SCATTERING STUDIES OF HUMAN ACETYLCHOLINESTERASE TO INFORM THE DESIGN OF OXIME REACTIVATORS. O Gerlits, M Fajer, X Cheng, D Blumenthal, P Taylor, Z Radić, ... Military Medical Science Letters/Vojenské Zdravotnické Listy 87, 2018 | | 2018 |