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@article{yu_toward_2019,
title = {Toward {Atomistic} {Modeling} of {Irreversible} {Covalent} {Inhibitor} {Binding} {Kinetics}},
volume = {59},
issn = {1549-9596, 1549-960X},
url = {https://pubs.acs.org/doi/10.1021/acs.jcim.9b00268},
doi = {10.1021/acs.jcim.9b00268},
language = {en},
number = {9},
urldate = {2022-04-06},
journal = {Journal of Chemical Information and Modeling},
author = {Yu, Haoyu S. and Gao, Cen and Lupyan, Dmitry and Wu, Yujie and Kimura, Takayuki and Wu, Chuanjie and Jacobson, Leif and Harder, Edward and Abel, Robert and Wang, Lingle},
month = sep,
year = {2019},
pages = {3955--3967},
}
@article{dorsch_identification_2015,
title = {Identification and Optimization of Pyridazinones as Potent and Selective c-{Met} Kinase Inhibitors},
volume = {25},
issn = {0960894X},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0960894X15000955},
doi = {10.1016/j.bmcl.2015.02.002},
language = {en},
number = {7},
urldate = {2020-12-10},
journal = {Bioorganic \& Medicinal Chemistry Letters},
author = {Dorsch, Dieter and Schadt, Oliver and Stieber, Frank and Meyring, Michael and Grädler, Ulrich and Bladt, Friedhelm and Friese-Hamim, Manja and Knühl, Christine and Pehl, Ulrich and Blaukat, Andree},
month = apr,
year = {2015},
pages = {1597--1602},
}
@article{crooks_pathensemble_2000,
title = {Path-Ensemble Averages in Systems Driven far from Equilibrium},
volume = {61},
issn = {1063-651X, 1095-3787},
url = {https://link.aps.org/doi/10.1103/PhysRevE.61.2361},
doi = {10.1103/PhysRevE.61.2361},
language = {en},
number = {3},
urldate = {2020-08-18},
journal = {Physical Review E},
author = {Crooks, Gavin E.},
month = mar,
year = {2000},
pages = {2361--2366},
}
@article{jorgensen_perspective_2008,
title = {Perspective on {Free}-{Energy} {Perturbation} {Calculations} for {Chemical} {Equilibria}},
volume = {4},
issn = {1549-9618, 1549-9626},
url = {https://pubs.acs.org/doi/10.1021/ct800011m},
doi = {10.1021/ct800011m},
language = {en},
number = {6},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Jorgensen, William L. and Thomas, Laura L.},
month = jun,
year = {2008},
pages = {869--876},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\XG2H8BWI\\Jorgensen and Thomas - 2008 - Perspective on Free-Energy Perturbation Calculatio.pdf:application/pdf},
}
@article{straatsma_free_1986,
title = {Free Energy of Hydrophobic Hydration: {A} Molecular Dynamics Study of Noble Gases in Water},
volume = {85},
issn = {0021-9606, 1089-7690},
shorttitle = {Free energy of hydrophobic hydration},
url = {http://aip.scitation.org/doi/10.1063/1.451846},
doi = {10.1063/1.451846},
language = {en},
number = {11},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Straatsma, T. P. and Berendsen, H. J. C. and Postma, J. P. M.},
month = dec,
year = {1986},
pages = {6720--6727},
file = {Full Text:C\:\\Users\\dhahn3\\Zotero\\storage\\58JT5WZA\\Straatsma et al. - 1986 - Free energy of hydrophobic hydration A molecular .pdf:application/pdf},
}
@article{hummer_fastgrowth_2002,
title = {Fast-Growth {Thermodynamic} {Integration}: {Results} for {Sodium} {Ion} {Hydration}},
volume = {28},
issn = {0892-7022, 1029-0435},
url = {https://www.tandfonline.com/doi/full/10.1080/08927020211972},
doi = {10.1080/08927020211972},
language = {en},
number = {1-2},
urldate = {2020-08-18},
journal = {Molecular Simulation},
author = {Hummer, Gerhard},
month = jan,
year = {2002},
pages = {81--90},
}
@article{hendrix_fast_2001,
title = {A “Fast Growth” Method of Computing Free Energy Differences},
volume = {114},
issn = {0021-9606, 1089-7690},
url = {http://aip.scitation.org/doi/10.1063/1.1353552},
doi = {10.1063/1.1353552},
language = {en},
number = {14},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Hendrix, D. A. and Jarzynski, C.},
month = apr,
year = {2001},
pages = {5974--5981},
file = {Submitted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\DFQBUKIS\\Hendrix and Jarzynski - 2001 - A “fast growth” method of computing free energy di.pdf:application/pdf},
}
@article{jarzynski_nonequilibrium_1997,
title = {Nonequilibrium {Equality} for {Free} {Energy} {Differences}},
volume = {78},
issn = {0031-9007, 1079-7114},
url = {https://link.aps.org/doi/10.1103/PhysRevLett.78.2690},
doi = {10.1103/PhysRevLett.78.2690},
language = {en},
number = {14},
urldate = {2020-08-18},
journal = {Physical Review Letters},
author = {Jarzynski, C.},
month = apr,
year = {1997},
pages = {2690--2693},
file = {Submitted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\5BEF9YRE\\Jarzynski - 1997 - Nonequilibrium Equality for Free Energy Difference.pdf:application/pdf},
}
@article{boresch_convergence_2017,
title = {Convergence of single-step free energy perturbation},
volume = {115},
issn = {0026-8976, 1362-3028},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2016.1269960},
doi = {10.1080/00268976.2016.1269960},
language = {en},
number = {9-12},
urldate = {2020-08-18},
journal = {Molecular Physics},
author = {Boresch, Stefan and Woodcock, H. Lee},
month = jun,
year = {2017},
pages = {1200--1213},
}
@article{perthold_accelerated_2018,
title = {Accelerated {Enveloping} {Distribution} {Sampling}: {Enabling} {Sampling} of {Multiple} {End} {States} while {Preserving} {Local} {Energy} {Minima}},
volume = {122},
issn = {1520-6106, 1520-5207},
shorttitle = {Accelerated {Enveloping} {Distribution} {Sampling}},
url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.8b02725},
doi = {10.1021/acs.jpcb.8b02725},
language = {en},
number = {19},
urldate = {2021-11-11},
journal = {The Journal of Physical Chemistry B},
author = {Perthold, Jan Walther and Oostenbrink, Chris},
month = may,
year = {2018},
pages = {5030--5037},
file = {Full Text:C\:\\Users\\dhahn3\\Zotero\\storage\\E28CCSPX\\Perthold and Oostenbrink - 2018 - Accelerated Enveloping Distribution Sampling Enab.pdf:application/pdf},
}
@article{tan_optimally_2017,
title = {Optimally {Adjusted} {Mixture} {Sampling} and {Locally} {Weighted} {Histogram} {Analysis}},
volume = {26},
issn = {1061-8600, 1537-2715},
url = {https://www.tandfonline.com/doi/full/10.1080/10618600.2015.1113975},
doi = {10.1080/10618600.2015.1113975},
language = {en},
number = {1},
urldate = {2021-11-11},
journal = {Journal of Computational and Graphical Statistics},
author = {Tan, Zhiqiang},
month = jan,
year = {2017},
pages = {54--65},
}
@article{christ_comparison_2009,
title = {Comparison of Three Enveloping Distribution Sampling {Hamiltonians} for the Estimation of Multiple Free Energy Differences from a Single Simulation},
volume = {30},
issn = {01928651, 1096987X},
url = {http://doi.wiley.com/10.1002/jcc.21325},
doi = {10.1002/jcc.21325},
language = {en},
number = {11},
urldate = {2020-08-18},
journal = {Journal of Computational Chemistry},
author = {Christ, Clara D. and Van Gunsteren, Wilfred F.},
month = aug,
year = {2009},
pages = {1664--1679},
}
@article{christ_simple_2009,
title = {Simple, {Efficient}, and {Reliable} {Computation} of {Multiple} {Free} {Energy} {Differences} from a {Single} {Simulation}: {A} {Reference} {Hamiltonian} {Parameter} {Update} {Scheme} for {Enveloping} {Distribution} {Sampling} ({EDS})},
volume = {5},
issn = {1549-9618, 1549-9626},
shorttitle = {Simple, {Efficient}, and {Reliable} {Computation} of {Multiple} {Free} {Energy} {Differences} from a {Single} {Simulation}},
url = {https://pubs.acs.org/doi/10.1021/ct800424v},
doi = {10.1021/ct800424v},
language = {en},
number = {2},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Christ, Clara D. and van Gunsteren, Wilfred F.},
month = feb,
year = {2009},
pages = {276--286},
}
@article{christ_multiple_2008,
title = {Multiple Free energies from a Single Simulation: {Extending} Enveloping Distribution Sampling to Nonoverlapping Phase-Space Distributions},
volume = {128},
issn = {0021-9606, 1089-7690},
shorttitle = {Multiple free energies from a single simulation},
url = {http://aip.scitation.org/doi/10.1063/1.2913050},
doi = {10.1063/1.2913050},
language = {en},
number = {17},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Christ, Clara D. and van Gunsteren, Wilfred F.},
month = may,
year = {2008},
pages = {174112},
}
@article{hansen_efficient_2013,
title = {Efficient {Combination} of {Environment} {Change} and {Alchemical} {Perturbation} within the {Enveloping} {Distribution} {Sampling} ({EDS}) {Scheme}: {Twin}-{System} {EDS} and {Application} to the {Determination} of {Octanol}–{Water} {Partition} {Coefficients}},
volume = {9},
issn = {1549-9618, 1549-9626},
shorttitle = {Efficient {Combination} of {Environment} {Change} and {Alchemical} {Perturbation} within the {Enveloping} {Distribution} {Sampling} ({EDS}) {Scheme}},
url = {https://pubs.acs.org/doi/10.1021/ct300933y},
doi = {10.1021/ct300933y},
language = {en},
number = {3},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Hansen, Niels and Hünenberger, Philippe H. and van Gunsteren, Wilfred F.},
month = mar,
year = {2013},
pages = {1334--1346},
}
@article{sidler_efficient_2017,
title = {Efficient {Round}-{Trip} {Time} {Optimization} for {Replica}-{Exchange} {Enveloping} {Distribution} {Sampling} ({RE}-{EDS})},
volume = {13},
issn = {1549-9618, 1549-9626},
url = {https://pubs.acs.org/doi/10.1021/acs.jctc.7b00286},
doi = {10.1021/acs.jctc.7b00286},
language = {en},
number = {6},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Sidler, Dominik and Cristòfol-Clough, Michael and Riniker, Sereina},
month = jun,
year = {2017},
pages = {3020--3030},
}
@article{christ_enveloping_2007,
title = {Enveloping Distribution Sampling: {A} Method to Calculate Free Energy Differences from a Single Simulation},
volume = {126},
issn = {0021-9606, 1089-7690},
shorttitle = {Enveloping distribution sampling},
url = {http://aip.scitation.org/doi/10.1063/1.2730508},
doi = {10.1063/1.2730508},
language = {en},
number = {18},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Christ, Clara D. and van Gunsteren, Wilfred F.},
month = may,
year = {2007},
pages = {184110},
}
@article{kong_dynamics_1996,
title = {$\lambda$‐Dynamics: {A} New Approach to Free Energy Calculations},
volume = {105},
issn = {0021-9606, 1089-7690},
shorttitle = {$\lambda$‐dynamics},
url = {http://aip.scitation.org/doi/10.1063/1.472109},
doi = {10.1063/1.472109},
language = {en},
number = {6},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Kong, Xianjun and Brooks, Charles L.},
month = aug,
year = {1996},
pages = {2414--2423},
}
@article{donnini_constant_2011,
title = {Constant {pH} {Molecular} {Dynamics} in {Explicit} {Solvent} with $\lambda$-{Dynamics}},
volume = {7},
issn = {1549-9618, 1549-9626},
url = {https://pubs.acs.org/doi/10.1021/ct200061r},
doi = {10.1021/ct200061r},
language = {en},
number = {6},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Donnini, Serena and Tegeler, Florian and Groenhof, Gerrit and Grubmüller, Helmut},
month = jun,
year = {2011},
pages = {1962--1978},
file = {Full Text:C\:\\Users\\dhahn3\\Zotero\\storage\\CVV5XJLH\\Donnini et al. - 2011 - Constant pH Molecular Dynamics in Explicit Solvent.pdf:application/pdf},
}
@article{raman_estimation_2017,
title = {Estimation of Relative Free Energies of Binding Using Pre-Computed Ensembles Based on the Single-Step Free Energy Perturbation and the Site-Identification by {Ligand} Competitive Saturation Approaches},
volume = {38},
issn = {01928651},
url = {http://doi.wiley.com/10.1002/jcc.24522},
doi = {10.1002/jcc.24522},
language = {en},
number = {15},
urldate = {2020-08-18},
journal = {Journal of Computational Chemistry},
author = {Raman, E. Prabhu and Lakkaraju, Sirish Kaushik and Denny, Rajiah Aldrin and MacKerell, Alexander D.},
month = jun,
year = {2017},
pages = {1238--1251},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\TVKDTIJV\\Raman et al. - 2017 - Estimation of relative free energies of binding us.pdf:application/pdf},
}
@article{raman_sitespecific_2012,
title = {Site-{Specific} {Fragment} {Identification} {Guided} by {Single}-{Step} {Free} {Energy} {Perturbation} {Calculations}},
volume = {8},
issn = {1549-9618, 1549-9626},
url = {https://pubs.acs.org/doi/10.1021/ct300088r},
doi = {10.1021/ct300088r},
language = {en},
number = {10},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Raman, E. Prabhu and Vanommeslaeghe, Kenno and MacKerell, Alexander D.},
month = oct,
year = {2012},
pages = {3513--3525},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\HAUHB3JD\\Raman et al. - 2012 - Site-Specific Fragment Identification Guided by Si.pdf:application/pdf},
}
@article{liu_estimating_1996,
title = {Estimating the {Relative} {Free} {Energy} of {Different} {Molecular} {States} with {Respect} to a {Single} {Reference} {State}},
volume = {100},
issn = {0022-3654, 1541-5740},
url = {https://pubs.acs.org/doi/10.1021/jp9605212},
doi = {10.1021/jp9605212},
language = {en},
number = {22},
urldate = {2020-08-18},
journal = {The Journal of Physical Chemistry},
author = {Liu, Haiyan and Mark, Alan E. and van Gunsteren, Wilfred F.},
month = jan,
year = {1996},
pages = {9485--9494},
}
@article{vilseck_predicting_2018,
title = {Predicting {Binding} {Free} {Energies} in a {Large} {Combinatorial} {Chemical} {Space} {Using} {Multisite} $\lambda$ {Dynamics}},
volume = {9},
issn = {1948-7185},
url = {https://pubs.acs.org/doi/10.1021/acs.jpclett.8b01284},
doi = {10.1021/acs.jpclett.8b01284},
language = {en},
number = {12},
urldate = {2020-08-18},
journal = {The Journal of Physical Chemistry Letters},
author = {Vilseck, Jonah Z. and Armacost, Kira A. and Hayes, Ryan L. and Goh, Garrett B. and Brooks, Charles L.},
month = jun,
year = {2018},
pages = {3328--3332},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\Z6L2BAWB\\Vilseck et al. - 2018 - Predicting Binding Free Energies in a Large Combin.pdf:application/pdf},
}
@article{hayes_adaptive_2017,
title = {Adaptive {Landscape} {Flattening} {Accelerates} {Sampling} of {Alchemical} {Space} in {Multisite} $\lambda$ {Dynamics}},
volume = {121},
issn = {1520-6106, 1520-5207},
url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.6b09656},
doi = {10.1021/acs.jpcb.6b09656},
language = {en},
number = {15},
urldate = {2020-08-18},
journal = {The Journal of Physical Chemistry B},
author = {Hayes, Ryan L. and Armacost, Kira A. and Vilseck, Jonah Z. and Brooks, Charles L.},
month = apr,
year = {2017},
pages = {3626--3635},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\L9I9GGMY\\Hayes et al. - 2017 - Adaptive Landscape Flattening Accelerates Sampling.pdf:application/pdf},
}
@article{armacost_biasing_2015,
title = {Biasing {Potential} {Replica} {Exchange} {Multisite} $\lambda$-{Dynamics} for {Efficient} {Free} {Energy} {Calculations}},
volume = {11},
issn = {1549-9618, 1549-9626},
url = {https://pubs.acs.org/doi/10.1021/ct500894k},
doi = {10.1021/ct500894k},
language = {en},
number = {3},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Armacost, Kira A. and Goh, Garrett B. and Brooks, Charles L.},
month = mar,
year = {2015},
pages = {1267--1277},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\RMREZ4FN\\Armacost et al. - 2015 - Biasing Potential Replica Exchange Multisite $\lambda$-Dyn.pdf:application/pdf},
}
@article{guo_rapid_1998,
title = {Rapid {Screening} of {Binding} {Affinities}: {Application} of the $\lambda$-{Dynamics} {Method} to a {Trypsin}-{Inhibitor} {System}},
volume = {120},
issn = {0002-7863, 1520-5126},
shorttitle = {Rapid {Screening} of {Binding} {Affinities}},
url = {https://pubs.acs.org/doi/10.1021/ja973418e},
doi = {10.1021/ja973418e},
language = {en},
number = {8},
urldate = {2020-08-18},
journal = {Journal of the American Chemical Society},
author = {Guo, Zhuyan and Brooks, Charles L.},
month = mar,
year = {1998},
pages = {1920--1921},
}
@article{guo_application_2003,
title = {Application of the $\lambda$-{Dynamics} {Method} {To} {Evaluate} the {Relative} {Binding} {Free} {Energies} of {Inhibitors} to {HCV} {Protease}},
volume = {46},
issn = {0022-2623, 1520-4804},
url = {https://pubs.acs.org/doi/10.1021/jm030040o},
doi = {10.1021/jm030040o},
language = {en},
number = {25},
urldate = {2020-08-18},
journal = {Journal of Medicinal Chemistry},
author = {Guo, Zhuyan and Durkin, James and Fischmann, Thierry and Ingram, Richard and Prongay, Andrew and Zhang, Rumin and Madison, Vincent},
month = dec,
year = {2003},
pages = {5360--5364},
}
@article{knight_applying_2011,
title = {Applying Efficient Implicit Nongeometric Constraints in Alchemical Free Energy Simulations},
volume = {32},
issn = {01928651},
url = {http://doi.wiley.com/10.1002/jcc.21921},
doi = {10.1002/jcc.21921},
language = {en},
number = {16},
urldate = {2020-08-18},
journal = {Journal of Computational Chemistry},
author = {Knight, Jennifer L. and Brooks, Charles L.},
month = dec,
year = {2011},
pages = {3423--3432},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\E5NDB6UF\\Knight and Brooks - 2011 - Applying efficient implicit nongeometric constrain.pdf:application/pdf},
}
@article{knight_multisite_2011,
title = {Multisite $\lambda$ {Dynamics} for {Simulated} {Structure}–{Activity} {Relationship} {Studies}},
volume = {7},
issn = {1549-9618, 1549-9626},
url = {https://pubs.acs.org/doi/10.1021/ct200444f},
doi = {10.1021/ct200444f},
language = {en},
number = {9},
urldate = {2020-08-18},
journal = {Journal of Chemical Theory and Computation},
author = {Knight, Jennifer L. and Brooks, Charles L.},
month = sep,
year = {2011},
pages = {2728--2739},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\2RHVQ94R\\Knight and Brooks - 2011 - Multisite $\lambda$ Dynamics for Simulated Structure–Activ.pdf:application/pdf},
}
@article{knight_ldynamics_2009,
title = {$\lambda$-{Dynamics} Free Energy Simulation Methods},
volume = {30},
issn = {01928651, 1096987X},
url = {http://doi.wiley.com/10.1002/jcc.21295},
doi = {10.1002/jcc.21295},
language = {en},
number = {11},
urldate = {2020-08-18},
journal = {Journal of Computational Chemistry},
author = {Knight, Jennifer L. and Brooks, Charles L.},
month = aug,
year = {2009},
pages = {1692--1700},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\KQ5B83V9\\Knight and Brooks - 2009 - $\lambda$-Dynamics free energy simulation methods.pdf:application/pdf},
}
@article{damodaran_application_2001,
title = {Application of {Multiple} {Topology} $\lambda$-{Dynamics} to a {Host}−{Guest} {System}: β-{Cyclodextrin} with {Substituted} {Benzenes}},
volume = {105},
issn = {1520-6106, 1520-5207},
shorttitle = {Application of {Multiple} {Topology} $\lambda$-{Dynamics} to a {Host}−{Guest} {System}},
url = {https://pubs.acs.org/doi/10.1021/jp010361g},
doi = {10.1021/jp010361g},
language = {en},
number = {38},
urldate = {2020-08-18},
journal = {The Journal of Physical Chemistry B},
author = {Damodaran, K. V. and Banba, Shinichi and Brooks, Charles L.},
month = sep,
year = {2001},
pages = {9316--9322},
}
@article{lyubartsev_determination_1996,
title = {Determination of {Free} {Energy} from {Chemical} {Potentials}: {Application} of the {Expanded} {Ensemble} {Method}},
volume = {18},
issn = {0892-7022, 1029-0435},
shorttitle = {Determination of {Free} {Energy} from {Chemical} {Potentials}},
url = {http://www.tandfonline.com/doi/abs/10.1080/08927029608022353},
doi = {10.1080/08927029608022353},
language = {en},
number = {1-2},
urldate = {2020-08-18},
journal = {Molecular Simulation},
author = {Lyubartsev, A. P. and Laaksonen, A. and Vorontsov-Velyaminov, P. N.},
month = sep,
year = {1996},
pages = {43--58},
}
@article{lyubartsev_free_1994,
title = {Free Energy Calculations for {Lennard}-{Jones} Systems and Water Using the Expanded Ensemble Method: {A} {Monte} {Carlo} and Molecular Dynamics Simulation Study},
volume = {82},
issn = {0026-8976, 1362-3028},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268979400100344},
doi = {10.1080/00268979400100344},
language = {en},
number = {3},
urldate = {2020-08-18},
journal = {Molecular Physics},
author = {Lyubartsev, Alexander P. and Laaksonen, Aatto and Vorontsov-Velyaminov, Pavel N.},
month = jun,
year = {1994},
pages = {455--471},
}
@article{lyubartsev_new_1992,
title = {New Approach to {Monte} {Carlo} Calculation of the Free Energy: {Method} of Expanded Ensembles},
volume = {96},
issn = {0021-9606, 1089-7690},
shorttitle = {New approach to {Monte} {Carlo} calculation of the free energy},
url = {http://aip.scitation.org/doi/10.1063/1.462133},
doi = {10.1063/1.462133},
language = {en},
number = {3},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Lyubartsev, A. P. and Martsinovski, A. A. and Shevkunov, S. V. and Vorontsov‐Velyaminov, P. N.},
month = feb,
year = {1992},
pages = {1776--1783},
}
@article{escobedo_optimized_2007,
title = {Optimized Expanded Ensembles for Simulations Involving Molecular Insertions and Deletions. {II}. {Open} Systems},
volume = {127},
issn = {0021-9606, 1089-7690},
url = {http://aip.scitation.org/doi/10.1063/1.2800321},
doi = {10.1063/1.2800321},
language = {en},
number = {17},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Escobedo, Fernando A.},
month = nov,
year = {2007},
pages = {174104},
}
@article{escobedo_optimized_2007a,
title = {Optimized Expanded Ensembles for Simulations Involving Molecular Insertions and Deletions. {I}. {Closed} Systems},
volume = {127},
issn = {0021-9606, 1089-7690},
url = {http://aip.scitation.org/doi/10.1063/1.2800320},
doi = {10.1063/1.2800320},
language = {en},
number = {17},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Escobedo, Fernando A. and Martínez-Veracoechea, Francisco J.},
month = nov,
year = {2007},
pages = {174103},
}
@article{sugita_replicaexchange_1999,
title = {Replica-exchange Molecular Dynamics Method for Protein Folding},
volume = {314},
issn = {00092614},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0009261499011239},
doi = {10.1016/S0009-2614(99)01123-9},
language = {en},
number = {1-2},
urldate = {2020-08-18},
journal = {Chemical Physics Letters},
author = {Sugita, Yuji and Okamoto, Yuko},
month = nov,
year = {1999},
pages = {141--151},
}
@article{fukunishi_hamiltonian_2002,
title = {On the {Hamiltonian} Replica Exchange Method for Efficient Sampling of Biomolecular Systems: {Application} to Protein Structure Prediction},
volume = {116},
issn = {0021-9606, 1089-7690},
shorttitle = {On the {Hamiltonian} replica exchange method for efficient sampling of biomolecular systems},
url = {http://aip.scitation.org/doi/10.1063/1.1472510},
doi = {10.1063/1.1472510},
language = {en},
number = {20},
urldate = {2020-08-18},
journal = {The Journal of Chemical Physics},
author = {Fukunishi, Hiroaki and Watanabe, Osamu and Takada, Shoji},
month = may,
year = {2002},
pages = {9058--9067},
}
@article{zhang_simulating_2016,
title = {Simulating {Replica} {Exchange}: {Markov} {State} {Models}, {Proposal} {Schemes}, and the {Infinite} {Swapping} {Limit}},
volume = {120},
issn = {1520-6106, 1520-5207},
shorttitle = {Simulating {Replica} {Exchange}},
url = {https://pubs.acs.org/doi/10.1021/acs.jpcb.6b02015},
doi = {10.1021/acs.jpcb.6b02015},
language = {en},
number = {33},
urldate = {2020-08-18},
journal = {The Journal of Physical Chemistry B},
author = {Zhang, Bin W. and Dai, Wei and Gallicchio, Emilio and He, Peng and Xia, Junchao and Tan, Zhiqiang and Levy, Ronald M.},
month = aug,
year = {2016},
pages = {8289--8301},
file = {Accepted Version:C\:\\Users\\dhahn3\\Zotero\\storage\\P2JYBHLX\\Zhang et al. - 2016 - Simulating Replica Exchange Markov State Models, .pdf:application/pdf},
}
@article{koeppl1967inversion,
title = {Inversion Barriers of Pyramidal ({XY3}) and Related Planar (={XY}) Species},
volume = {89},
issn = {0002-7863, 1520-5126},
url = {https://pubs.acs.org/doi/abs/10.1021/ja00990a004},
doi = {10.1021/ja00990a004},
language = {en},
number = {14},
urldate = {2022-08-29},
journal = {Journal of the American Chemical Society},
author = {Koeppl, Gerald W. and Sagatys, Dalius S. and Krishnamurthy, G. S. and Miller, Sidney Israel.},
month = jul,
year = {1967},
pages = {3396--3405},
}
@article{genheden_mm_2015,
title = {The {MM}/{PBSA} and {MM}/{GBSA} methods to estimate ligand-binding affinities},
volume = {10},
issn = {1746-0441, 1746-045X},
url = {http://www.tandfonline.com/doi/full/10.1517/17460441.2015.1032936},
doi = {10.1517/17460441.2015.1032936},
language = {en},
number = {5},
urldate = {2021-05-13},
journal = {Expert Opinion on Drug Discovery},
author = {Genheden, Samuel and Ryde, Ulf},
month = may,
year = {2015},
pages = {449--461},
file = {Full Text:C\:\\Users\\dhahn3\\Zotero\\storage\\QJS4JE3P\\Genheden and Ryde - 2015 - The MMPBSA and MMGBSA methods to estimate ligand.pdf:application/pdf},
}
@article{madhavisastry_protein_2013,
title = {Protein and Ligand Preparation: Parameters, Protocols, and Influence on Virtual Screening Enrichments},
shorttitle = {Protein and Ligand Preparation},
author = {Madhavi Sastry, G. and Adzhigirey, Matvey and Day, Tyler and Annabhimoju, Ramakrishna and Sherman, Woody},
year = {2013},
month = mar,
volume = {27},
pages = {221--234},
issn = {0920-654X, 1573-4951},
doi = {10.1007/s10822-013-9644-8},
journal = {Journal of Computer-Aided Molecular Design},
language = {en},
number = {3}
}
@misc{moe_2021,
title = {Molecular {{Operating Environment}} ({{MOE}})},
shorttitle = {{{MOE}}},
year = {2022},
address = {{1010 Sherbooke St. West, Suite \#910, Montreal, QC, Canada, H3A 2R7}},
howpublished = {Chemical Computing Group ULC.}
}
@misc{openeye_spruce,
title = {{{Spruce 1.5.0.1}}},
url = {http://www.eyesopen.com},
address = {{Santa Fe, NM}},
howpublished = {OpenEye Scientific Software}
}
@article{meyder_estimating_2017,
title = {Estimating {{Electron Density Support}} for {{Individual Atoms}} and {{Molecular Fragments}} in {{X}}-Ray {{Structures}}},
author = {Meyder, Agnes and Nittinger, Eva and Lange, Gudrun and Klein, Robert and Rarey, Matthias},
year = {2017},
month = oct,
volume = {57},
pages = {2437--2447},
issn = {1549-9596, 1549-960X},
doi = {10.1021/acs.jcim.7b00391},
journal = {Journal of Chemical Information and Modeling},
language = {en},
number = {10}
}
@article{tickle_statistical_2012,
title = {Statistical Quality Indicators for Electron-Density Maps},
author = {Tickle, I. J.},
year = {2012},
month = apr,
volume = {68},
pages = {454--467},
publisher = {{International Union of Crystallography}},
issn = {0907-4449},
doi = {10.1107/S0907444911035918},
abstract = {A likelihood-based metric for scoring the local agreement of a structure model with the observed electron density is described.},
copyright = {https://creativecommons.org/licenses/by/2.0/uk},
file = {D\:\\Users\\DHahn3\\Zotero\\storage\\GZZDD8UX\\Tickle - 2012 - Statistical quality indicators for electron-densit.pdf;D\:\\Users\\DHahn3\\Zotero\\storage\\M3QRZE7E\\paper.html},
journal = {Acta Crystallographica Section D: Biological Crystallography},
language = {en},
number = {4}
}
@article{ono_improvement_2020,
title = {Improvement in Predicting Drug Sensitivity Changes Associated with Protein Mutations Using a Molecular Dynamics Based Alchemical Mutation Method},
author = {Ono, Fumie and Chiba, Shuntaro and Isaka, Yuta and Matsumoto, Shigeyuki and Ma, Biao and Katayama, Ryohei and Araki, Mitsugu and Okuno, Yasushi},
year = {2020},
month = feb,
volume = {10},
pages = {2161},
publisher = {{Nature Publishing Group}},
issn = {2045-2322},
doi = {10.1038/s41598-020-58877-9},
abstract = {While molecular-targeted drugs have demonstrated strong therapeutic efficacy against diverse diseases such as cancer and infection, the appearance of drug resistance associated with genetic variations in individual patients or pathogens has severely limited their clinical efficacy. Therefore, precision medicine approaches based on the personal genomic background provide promising strategies to enhance the effectiveness of molecular-targeted therapies. However, identifying drug resistance mutations in individuals by combining DNA sequencing and in vitro analyses is generally time consuming and costly. In contrast, in silico computation of protein-drug binding free energies allows for the rapid prediction of drug sensitivity changes associated with specific genetic mutations. Although conventional alchemical free energy computation methods have been used to quantify mutation-induced drug sensitivity changes in some protein targets, these methods are often adversely affected by free energy convergence. In this paper, we demonstrate significant improvements in prediction performance and free energy convergence by employing an alchemical mutation protocol, MutationFEP, which directly estimates binding free energy differences associated with protein mutations in three types of a protein and drug system. The superior performance of MutationFEP appears to be attributable to its more-moderate perturbation scheme. Therefore, this study provides a deeper level of insight into computer-assisted precision medicine.},
copyright = {2020 The Author(s)},
file = {D\:\\Users\\DHahn3\\Zotero\\storage\\J6EKA3BV\\Ono et al. - 2020 - Improvement in predicting drug sensitivity changes.pdf;D\:\\Users\\DHahn3\\Zotero\\storage\\9JPJR7HC\\s41598-020-58877-9.html},
journal = {Scientific Reports},
language = {en},
number = {1}
}
@article{rocklin_calculating_2013,
title = {Calculating the Binding Free Energies of Charged Species Based on Explicit-Solvent Simulations Employing Lattice-Sum Methods: {{An}} Accurate Correction Scheme for Electrostatic Finite-Size Effects},
shorttitle = {Calculating the Binding Free Energies of Charged Species Based on Explicit-Solvent Simulations Employing Lattice-Sum Methods},
author = {Rocklin, Gabriel J. and Mobley, David L. and Dill, Ken A. and H{\"u}nenberger, Philippe H.},
year = {2013},
month = nov,
volume = {139},
pages = {184103},
issn = {0021-9606},
doi = {10.1063/1.4826261},
journal = {The Journal of Chemical Physics},
number = {18}
}
@article{swiderek_binding_2011,
title = {Binding {{Ligands}} and {{Cofactor}} to {{L}}-{{Lactate Dehydrogenase}} from {{Human Skeletal}} and {{Heart Muscles}}},
author = {{\'S}widerek, Katarzyna and Paneth, Piotr},
year = {2011},
month = may,
volume = {115},
pages = {6366--6376},
issn = {1520-6106},
doi = {10.1021/jp201626k},
abstract = {Binding affinities of cofactor and ligands to the active site of two different isoforms of lactate dehydrogenase (LDH), heart and skeletal muscles (H4 and M4, respectively), can be used for medical and biological applications. Herein, a hybrid QM/MM computational approach based on free energy perturbation methods has been carried out to estimate binding affinities and binding isotope effects (BIEs) for NADH/NAD+ and oxamate, pyruvate, L-lactate, and D-lactate ligands to the M4 and H4 isoforms of L-LDH. Here, we show that determining how cofactor and ligands interact with the active site of LDH isoforms advanced the still open discussion on the intracellular lactate shuttle hypothesis. In our discussion we deny the key concept of this hypothesis showing, based on interaction energy values, that there is no evidence that the M4 type of LDH in the skeletal muscles cells served as a catalyst of the conversion of lactate to pyruvate. Additionally, theoretical determination of BIEs for H4 and M4 types of LDH shows that there is a way of using the BIEs as a tool capable to distinguish these isoforms, and for this purpose D-lactate labeled with deuterium in positions 11 or 7, 8, 9 ([11-2H]-BIE and [7,8,9-2H3]-BIE) or L-lactate labeled only in position 11 ([11-2H]-BIE) could be used. We propose the BIEs as a useful tool which can be applied in order to experimentally determine the types of LDH.},
journal = {The Journal of Physical Chemistry B},
number = {19}
}
@article{tsai_validation_2020,
title = {Validation of {{Free Energy Methods}} in {{AMBER}}},
author = {Tsai, Hsu-Chun and Tao, Yujun and Lee, Tai-Sung and Merz, Kenneth M. and York, Darrin M.},
year = {2020},
month = nov,
volume = {60},
pages = {5296--5300},
publisher = {{American Chemical Society}},
issn = {1549-9596},
doi = {10.1021/acs.jcim.0c00285},
abstract = {Herein we provide high-precision validation tests of the latest GPU-accelerated free energy code in AMBER. We demonstrate that consistent free energy results are obtained in both the gas phase and in solution. We first show, in the context of thermodynamic integration (TI), that the results are invariant with respect to ``split'' (e.g., stepwise decharge\textendash vdW\textendash recharge) versus ``unified'' protocols. This brought to light a subtle inconsistency in previous versions of AMBER that was traced to the improper treatment of 1\textendash 4 vdW and electrostatic interactions involving atoms across the softcore boundary. We illustrate that under the assumption that the ensembles produced by different legs of the alchemical transformation between molecules A and B in the gas phase and aqueous phase are very small, the inconsistency in the relative hydration free energy {$\Delta\Delta$}Ghydr[A \textrightarrow{} B] = {$\Delta$}Gaq[A \textrightarrow{} B] \textendash{} {$\Delta$}Ggas[A \textrightarrow{} B] is minimal. However, for general cases where the ensembles are shown to be substantially different, as expected in ligand\textendash protein binding applications, these errors can be large. Finally, we demonstrate that results for relative hydration free energy simulations are independent of TI or multistate Bennett's acceptance ratio (MBAR) analysis, invariant to the specific choice of the softcore region, and in agreement with results derived from absolute hydration free energy values.},
file = {D\:\\Users\\DHahn3\\Zotero\\storage\\HBZXV9JE\\Tsai et al. - 2020 - Validation of Free Energy Methods in AMBER.pdf;D\:\\Users\\DHahn3\\Zotero\\storage\\BAKUUHI7\\acs.jcim.html},
journal = {Journal of Chemical Information and Modeling},
number = {11}
}
@article{vangunsteren_validation_2018,
title = {Validation of {{Molecular Simulation}}: {{An Overview}} of {{Issues}}},
shorttitle = {Validation of {{Molecular Simulation}}},
author = {{van Gunsteren}, Wilfred F. and Daura, Xavier and Hansen, Niels and Mark, Alan E. and Oostenbrink, Chris and Riniker, Sereina and Smith, Lorna J.},
year = {2018},
volume = {57},
pages = {884--902},
issn = {1521-3773},
doi = {10.1002/anie.201702945},
abstract = {Computer simulation of molecular systems enables structure\textendash energy\textendash function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp, 2) the accuracy of the function Q(rN) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN) to the configuration rN, 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.},
annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201702945},
file = {D\:\\Users\\DHahn3\\Zotero\\storage\\KGWCLEL6\\van Gunsteren et al. - 2018 - Validation of Molecular Simulation An Overview of.pdf;D\:\\Users\\DHahn3\\Zotero\\storage\\4PH3BINM\\anie.html},
journal = {Angewandte Chemie International Edition},
keywords = {computer chemistry,experimental data,molecular dynamics simulation,Monte Carlo simulation,pseudo-validation},
language = {en},
number = {4}
}
@article{baum_more_2009,
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title = {Discovery and {{Optimization}} of 2-{{Arylquinazolin}}-4-Ones into a {{Potent}} and {{Selective Tankyrase Inhibitor Modulating Wnt Pathway Activity}}},
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title = {Application of {{Free Energy Perturbation}} for the {{Design}} of {{BACE1 Inhibitors}}},
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number = {9}
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ids = {cumming\_structure\_2012a},
title = {Structure Based Design of Iminohydantoin {{BACE1}} Inhibitors: {{Identification}} of an Orally Available, Centrally Active {{BACE1}} Inhibitor},
shorttitle = {Structure Based Design of Iminohydantoin {{BACE1}} Inhibitors},
author = {Cumming, Jared N. and Smith, Elizabeth M. and Wang, Lingyan and Misiaszek, Jeffrey and Durkin, James and Pan, Jianping and Iserloh, Ulrich and Wu, Yusheng and Zhu, Zhaoning and Strickland, Corey and Voigt, Johannes and Chen, Xia and Kennedy, Matthew E. and Kuvelkar, Reshma and Hyde, Lynn A. and Cox, Kathleen and Favreau, Leonard and Czarniecki, Michael F. and Greenlee, William J. and McKittrick, Brian A. and Parker, Eric M. and Stamford, Andrew W.},
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title = {Galectin-3-{{Binding Glycomimetics}} That {{Strongly Reduce Bleomycin}}-{{Induced Lung Fibrosis}} and {{Modulate Intracellular Glycan Recognition}}},
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ids = {friberg\_discovery\_2013a},
title = {Discovery of {{Potent Myeloid Cell Leukemia}} 1 ({{Mcl}}-1) {{Inhibitors Using Fragment}}-{{Based Methods}} and {{Structure}}-{{Based Design}}},
author = {Friberg, Anders and Vigil, Dominico and Zhao, Bin and Daniels, R. Nathan and Burke, Jason P. and {Garcia-Barrantes}, Pedro M. and Camper, DeMarco and Chauder, Brian A. and Lee, Taekyu and Olejniczak, Edward T. and Fesik, Stephen W.},
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journal = {Journal of Medicinal Chemistry},
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number = {1}
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@article{gapsys_large_2020,
ids = {gapsys\_large\_2020a,gapsys\_large\_2020b},
title = {Large Scale Relative Protein Ligand Binding Affinities Using Non-Equilibrium Alchemy},