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 | 146 | 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 | 111 | 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 | 102 | 2008 |
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 | 54 | 2017 |
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 | 52 | 2007 |
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 | 43 | 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 | 32 | 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 | 17 | 2021 |
Full atom simulations of spin label conformations P Fajer, M Fajer, M Zawrotny, W Yang Methods in enzymology 563, 623-642, 2015 | 14 | 2015 |
Quantitatively accounting for protein reorganization in computer-aided drug design M Fajer, K Borrelli, R Abel, L Wang Journal of Chemical Theory and Computation 19 (11), 3080-3090, 2023 | 10 | 2023 |
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 | 9 | 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 |
Molecular modeling of spin labels M Fajer, PG Fajer, KL Sale ESR spectroscopy in membrane biophysics. Springer, New York, 253-259, 2007 | 7 | 2007 |
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 | 5 | 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 |
Leveraging the Thermodynamics of Protein Conformations in Drug Discovery BW Zhang, M Fajer, W Chen, F Moraca, L Wang Journal of Chemical Information and Modeling 65 (1), 252-264, 2024 | | 2024 |