85. Schöller, A.; H. Lee Woodcock; Boresch, S. Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes. Molecules 2023, 28, 4006 (DOI: 10.3390/molecules28104006).
84. Tkaczyk, S.; Karwounopoulos, J.; Schöller, A.; H. Lee Woodcock.; Langer, T.; Boresch, S.; Wieder, M. Using Neural Network Potentials to Efficiently Calculate Indirect Free Energy Estimates. ChemRxiv 2023. This content is a preprint and has not been peer-reviewed (DOI: 10.26434/chemrxiv-2023-qq206).
83. L.C. Warrensford, A.R. Pittman, F.L. Kearns, J. Hale, K. Astronskas, S.L. Austin, R.M. Young, A.L. Allcock, S.G. Dietrick, B.J. Baker, H. Lee Woodcock;* Identification of Potential SARS-CoV-2 Inhibitors Using Flexible Docking Based Drug Repurposing of Antivirals. ChemRxiv, 2022, This content is a preprint and has not been peer-reviewed (DOI: 10.26434/chemrxiv-2022-3zrrl).
82. P. S. Hudson, F. Aviat, R. Meana-Paneda, L. C. Warrensford, B. C. Pollard, S. Prasad, M. R. Jones, H. Lee Woodcock, B. R. Brooks. Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J. Comput. Aided Mol. Des., 2022 (DOI: 10.1007/s10822-022-00443-8).
81. A. Schöller, F.L. Kearns, H. Lee Woodcock,* S. Boresch;* Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations. J. Phys. Chem. B, 2022, 126, 2798-2811 (DOI: 10.1021/acs.jpcb.2c00696).
80. N.E. Avalon, J. Nafie, C. De Marco Verissimo, L.C. Warrensford, S. G. Dietrick, A.R. Pittman, R.M. Young, F.L. Kearns, T. Smalley, J.M. Binning, J.P. Dalton, M.P. Johnson, H. Lee Woodcock, A.L. Allcock, B.J. Baker; Tuaimenal A, a Meroterpene from the Irish Deep-Sea Soft Coral Duva florida, Displays Inhibition of the SARS-CoV-2 3CLpro Enzyme. J. Nat. Prod., 2022, In Press (DOI: 10.1021/acs.jnatprod.2c00054).
79. Vankayala, S. L., Warrensford, L. C., Pittman, A. R., Pollard, B. C., Kearns, F. L., Larkin, J. D., H. Lee Woodcock;* CIFDock: A novel CHARMM-based flexible receptor–flexible ligand docking protocol. J. Comput. Chem. 2022, 43(2), 84 (DOI: 10.1002/jcc.26759).
78. Laguionie-Marchais C, Allcock AL, Baker BJ, Conneely E-A, Dietrick SG, Kearns F, McKeever K, Young RM, Sierra CA, Soldatou S, H. Lee Woodcock, Johnson MP. Not Drug-like, but Like Drugs: Cnidaria Natural Products. Marine Drugs. 2022; 20(1):42 (DOI: 10.3390/md20010042).
77. Evgeny Epifanovsky, Andrew Gilbert, Xiaoliang Pan, Yihan Shao, H. Lee Woodcock. Technical Report: Integrated Web User Interface for Multi-Scale Chemical Physics Simulations (DE-SC0011297). United States: N. p., 2021.
76. András Szabadi, Roman Elfgen, Roberto Macchieraldo, Fiona L. Kearns, H. Lee Woodcock, Barbara Kirchner, Christian Schröder;* Comparison between ab initio and polarizable molecular dynamics simulations of 1-butyl-3-methylimidazolium tetrafluoroborate and chloride in water. Journal of Molecular Liquids, 2021, 337, 116521 (DOI: 10.1016/j.molliq.2021.116521).
75. Evgeny Epifanovsky, Andrew T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, Narbe Mardirossian, Pavel Pokhilko, Alec F. White, Marc P. Coons, Adrian L. Dempwolff, Zhengting Gan, Diptarka Hait, Paul R. Horn, Leif D. Jacobson, Ilya Kaliman, Jörg Kussmann, Adrian W. Lange, Ka Un Lao, Daniel S. Levine, Jie Liu, Simon C. McKenzie, Adrian F. Morrison, Kaushik D. Nanda, Felix Plasser, Dirk R. Rehn, Marta L. Vidal, Zhi-Qiang You, Ying Zhu, Bushra Alam, Benjamin J. Albrecht, Abdulrahman Aldossary, Ethan Alguire, Josefine H. Andersen, Vishikh Athavale, Dennis Barton, Khadiza Begam, Andrew Behn, Nicole Bellonzi, Yves A. Bernard, Eric J. Berquist, Hugh G. A. Burton, Abel Carreras, Kevin Carter-Fenk, Romit Chakraborty, Alan D. Chien, Kristina D. Closser, Vale Cofer-Shabica, Saswata Dasgupta, Marc de Wergifosse, Jia Deng, Michael Diedenhofen, Hainam Do, Sebastian Ehlert, Po-Tung Fang, Shervin Fatehi, Qingguo Feng, Triet Friedhoff, James Gayvert, Qinghui Ge, Gergely Gidofalvi, Matthew Goldey, Joe Gomes, Cristina E. González-Espinoza, Sahil Gulania, Anastasia O. Gunina, Magnus W. D. Hanson-Heine, Phillip H. P. Harbach, Andreas Hauser, Michael F. Herbst, Mario Hernández Vera, Manuel Hodecker, Zachary C. Holden, Shannon Houck, Xunkun Huang, Kerwin Hui, Bang C. Huynh, Maxim Ivanov, Ádám Jász, Hyunjun Ji, Hanjie Jiang, Benjamin Kaduk, Sven Kähler, Kirill Khistyaev, Jaehoon Kim, Gergely Kis, Phil Klunzinger, Zsuzsanna Koczor-Benda, Joong Hoon Koh, Dimitri Kosenkov, Laura Koulias, Tim Kowalczyk, Caroline M. Krauter, Karl Kue, Alexander Kunitsa, Thomas Kus, István Ladjánszki, Arie Landau, Keith V. Lawler, Daniel Lefrancois, Susi Lehtola, Run R. Li, Yi-Pei Li, Jiashu Liang, Marcus Liebenthal, Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, Matthias Loipersberger, Arne Luenser, Aaditya Manjanath, Prashant Manohar, Erum Mansoor, Sam F. Manzer, Shan-Ping Mao, Aleksandr V. Marenich, Thomas Markovich, Stephen Mason, Simon A. Maurer, Peter F. McLaughlin, Maximilian F. S. J. Menger, Jan-Michael Mewes, Stefanie A. Mewes, Pierpaolo Morgante, J. Wayne Mullinax, Katherine J. Oosterbaan, Garrette Paran, Alexander C. Paul, Suranjan K. Paul, Fabijan Pavošević, Zheng Pei, Stefan Prager, Emil I. Proynov, Ádám Rák, Eloy Ramos-Cordoba, Bhaskar Rana, Alan E. Rask, Adam Rettig, Ryan M. Richard, Fazle Rob, Elliot Rossomme, Tarek Scheele, Maximilian Scheurer, Matthias Schneider, Nickolai Sergueev, Shaama M. Sharada, Wojciech Skomorowski, David W. Small, Christopher J. Stein, Yu-Chuan Su, Eric J. Sundstrom, Zhen Tao, Jonathan Thirman, Gábor J. Tornai, Takashi Tsuchimochi, Norm M. Tubman, Srimukh Prasad Veccham, Oleg Vydrov, Jan Wenzel, Jon Witte, Atsushi Yamada, Kun Yao, Sina Yeganeh, Shane R. Yost, Alexander Zech, Igor Ying Zhang, Xing Zhang, Yu Zhang, Dmitry Zuev, Alán Aspuru-Guzik, Alexis T. Bell, Nicholas A. Besley, Ksenia B. Bravaya, Bernard R. Brooks, David Casanova, Jeng-Da Chai, Sonia Coriani, Christopher J. Cramer, György Cserey, A. Eugene DePrince III, Robert A. DiStasio Jr., Andreas Dreuw, Barry D. Dunietz, Thomas R. Furlani, William A. Goddard III, Sharon Hammes-Schiffer, Teresa Head-Gordon, Warren J. Hehre, Chao-Ping Hsu, Thomas-C. Jagau, Yousung Jung, Andreas Klamt, Jing Kong, Daniel S. Lambrecht, WanZhen Liang, Nicholas J. Mayhall, C. William McCurdy, Jeffrey B. Neaton, Christian Ochsenfeld, John A. Parkhill, Roberto Peverati, Vitaly A. Rassolov, Yihan Shao, Lyudmila V. Slipchenko, Tim Stauch, Ryan P. Steele, Joseph E. Subotnik, Alex J. W. Thom, Alexandre Tkatchenko, Donald G. Truhlar, Troy Van Voorhis, Tomasz A. Wesolowski, K. Birgitta Whaley, H. Lee Woodcock III, Paul M. Zimmerman, Shirin Faraji, Peter M. W. Gill, Martin Head-Gordon, John M. Herbert, and Anna I. Krylov , Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package, J. Chem. Phys., 2021, 155, 084801 (DOI: 10.1063/5.0055522).
84. Tkaczyk, S.; Karwounopoulos, J.; Schöller, A.; H. Lee Woodcock.; Langer, T.; Boresch, S.; Wieder, M. Using Neural Network Potentials to Efficiently Calculate Indirect Free Energy Estimates. ChemRxiv 2023. This content is a preprint and has not been peer-reviewed (DOI: 10.26434/chemrxiv-2023-qq206).
83. L.C. Warrensford, A.R. Pittman, F.L. Kearns, J. Hale, K. Astronskas, S.L. Austin, R.M. Young, A.L. Allcock, S.G. Dietrick, B.J. Baker, H. Lee Woodcock;* Identification of Potential SARS-CoV-2 Inhibitors Using Flexible Docking Based Drug Repurposing of Antivirals. ChemRxiv, 2022, This content is a preprint and has not been peer-reviewed (DOI: 10.26434/chemrxiv-2022-3zrrl).
82. P. S. Hudson, F. Aviat, R. Meana-Paneda, L. C. Warrensford, B. C. Pollard, S. Prasad, M. R. Jones, H. Lee Woodcock, B. R. Brooks. Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J. Comput. Aided Mol. Des., 2022 (DOI: 10.1007/s10822-022-00443-8).
81. A. Schöller, F.L. Kearns, H. Lee Woodcock,* S. Boresch;* Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations. J. Phys. Chem. B, 2022, 126, 2798-2811 (DOI: 10.1021/acs.jpcb.2c00696).
80. N.E. Avalon, J. Nafie, C. De Marco Verissimo, L.C. Warrensford, S. G. Dietrick, A.R. Pittman, R.M. Young, F.L. Kearns, T. Smalley, J.M. Binning, J.P. Dalton, M.P. Johnson, H. Lee Woodcock, A.L. Allcock, B.J. Baker; Tuaimenal A, a Meroterpene from the Irish Deep-Sea Soft Coral Duva florida, Displays Inhibition of the SARS-CoV-2 3CLpro Enzyme. J. Nat. Prod., 2022, In Press (DOI: 10.1021/acs.jnatprod.2c00054).
79. Vankayala, S. L., Warrensford, L. C., Pittman, A. R., Pollard, B. C., Kearns, F. L., Larkin, J. D., H. Lee Woodcock;* CIFDock: A novel CHARMM-based flexible receptor–flexible ligand docking protocol. J. Comput. Chem. 2022, 43(2), 84 (DOI: 10.1002/jcc.26759).
78. Laguionie-Marchais C, Allcock AL, Baker BJ, Conneely E-A, Dietrick SG, Kearns F, McKeever K, Young RM, Sierra CA, Soldatou S, H. Lee Woodcock, Johnson MP. Not Drug-like, but Like Drugs: Cnidaria Natural Products. Marine Drugs. 2022; 20(1):42 (DOI: 10.3390/md20010042).
77. Evgeny Epifanovsky, Andrew Gilbert, Xiaoliang Pan, Yihan Shao, H. Lee Woodcock. Technical Report: Integrated Web User Interface for Multi-Scale Chemical Physics Simulations (DE-SC0011297). United States: N. p., 2021.
76. András Szabadi, Roman Elfgen, Roberto Macchieraldo, Fiona L. Kearns, H. Lee Woodcock, Barbara Kirchner, Christian Schröder;* Comparison between ab initio and polarizable molecular dynamics simulations of 1-butyl-3-methylimidazolium tetrafluoroborate and chloride in water. Journal of Molecular Liquids, 2021, 337, 116521 (DOI: 10.1016/j.molliq.2021.116521).
75. Evgeny Epifanovsky, Andrew T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, Narbe Mardirossian, Pavel Pokhilko, Alec F. White, Marc P. Coons, Adrian L. Dempwolff, Zhengting Gan, Diptarka Hait, Paul R. Horn, Leif D. Jacobson, Ilya Kaliman, Jörg Kussmann, Adrian W. Lange, Ka Un Lao, Daniel S. Levine, Jie Liu, Simon C. McKenzie, Adrian F. Morrison, Kaushik D. Nanda, Felix Plasser, Dirk R. Rehn, Marta L. Vidal, Zhi-Qiang You, Ying Zhu, Bushra Alam, Benjamin J. Albrecht, Abdulrahman Aldossary, Ethan Alguire, Josefine H. Andersen, Vishikh Athavale, Dennis Barton, Khadiza Begam, Andrew Behn, Nicole Bellonzi, Yves A. Bernard, Eric J. Berquist, Hugh G. A. Burton, Abel Carreras, Kevin Carter-Fenk, Romit Chakraborty, Alan D. Chien, Kristina D. Closser, Vale Cofer-Shabica, Saswata Dasgupta, Marc de Wergifosse, Jia Deng, Michael Diedenhofen, Hainam Do, Sebastian Ehlert, Po-Tung Fang, Shervin Fatehi, Qingguo Feng, Triet Friedhoff, James Gayvert, Qinghui Ge, Gergely Gidofalvi, Matthew Goldey, Joe Gomes, Cristina E. González-Espinoza, Sahil Gulania, Anastasia O. Gunina, Magnus W. D. Hanson-Heine, Phillip H. P. Harbach, Andreas Hauser, Michael F. Herbst, Mario Hernández Vera, Manuel Hodecker, Zachary C. Holden, Shannon Houck, Xunkun Huang, Kerwin Hui, Bang C. Huynh, Maxim Ivanov, Ádám Jász, Hyunjun Ji, Hanjie Jiang, Benjamin Kaduk, Sven Kähler, Kirill Khistyaev, Jaehoon Kim, Gergely Kis, Phil Klunzinger, Zsuzsanna Koczor-Benda, Joong Hoon Koh, Dimitri Kosenkov, Laura Koulias, Tim Kowalczyk, Caroline M. Krauter, Karl Kue, Alexander Kunitsa, Thomas Kus, István Ladjánszki, Arie Landau, Keith V. Lawler, Daniel Lefrancois, Susi Lehtola, Run R. Li, Yi-Pei Li, Jiashu Liang, Marcus Liebenthal, Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, Matthias Loipersberger, Arne Luenser, Aaditya Manjanath, Prashant Manohar, Erum Mansoor, Sam F. Manzer, Shan-Ping Mao, Aleksandr V. Marenich, Thomas Markovich, Stephen Mason, Simon A. Maurer, Peter F. McLaughlin, Maximilian F. S. J. Menger, Jan-Michael Mewes, Stefanie A. Mewes, Pierpaolo Morgante, J. Wayne Mullinax, Katherine J. Oosterbaan, Garrette Paran, Alexander C. Paul, Suranjan K. Paul, Fabijan Pavošević, Zheng Pei, Stefan Prager, Emil I. Proynov, Ádám Rák, Eloy Ramos-Cordoba, Bhaskar Rana, Alan E. Rask, Adam Rettig, Ryan M. Richard, Fazle Rob, Elliot Rossomme, Tarek Scheele, Maximilian Scheurer, Matthias Schneider, Nickolai Sergueev, Shaama M. Sharada, Wojciech Skomorowski, David W. Small, Christopher J. Stein, Yu-Chuan Su, Eric J. Sundstrom, Zhen Tao, Jonathan Thirman, Gábor J. Tornai, Takashi Tsuchimochi, Norm M. Tubman, Srimukh Prasad Veccham, Oleg Vydrov, Jan Wenzel, Jon Witte, Atsushi Yamada, Kun Yao, Sina Yeganeh, Shane R. Yost, Alexander Zech, Igor Ying Zhang, Xing Zhang, Yu Zhang, Dmitry Zuev, Alán Aspuru-Guzik, Alexis T. Bell, Nicholas A. Besley, Ksenia B. Bravaya, Bernard R. Brooks, David Casanova, Jeng-Da Chai, Sonia Coriani, Christopher J. Cramer, György Cserey, A. Eugene DePrince III, Robert A. DiStasio Jr., Andreas Dreuw, Barry D. Dunietz, Thomas R. Furlani, William A. Goddard III, Sharon Hammes-Schiffer, Teresa Head-Gordon, Warren J. Hehre, Chao-Ping Hsu, Thomas-C. Jagau, Yousung Jung, Andreas Klamt, Jing Kong, Daniel S. Lambrecht, WanZhen Liang, Nicholas J. Mayhall, C. William McCurdy, Jeffrey B. Neaton, Christian Ochsenfeld, John A. Parkhill, Roberto Peverati, Vitaly A. Rassolov, Yihan Shao, Lyudmila V. Slipchenko, Tim Stauch, Ryan P. Steele, Joseph E. Subotnik, Alex J. W. Thom, Alexandre Tkatchenko, Donald G. Truhlar, Troy Van Voorhis, Tomasz A. Wesolowski, K. Birgitta Whaley, H. Lee Woodcock III, Paul M. Zimmerman, Shirin Faraji, Peter M. W. Gill, Martin Head-Gordon, John M. Herbert, and Anna I. Krylov , Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package, J. Chem. Phys., 2021, 155, 084801 (DOI: 10.1063/5.0055522).
73. V. Zeindlhofer, P. S. Hudson, A. M. Palvolgyi, M. Welsch, M. Almarashi, H. Lee Woodcock, B. R. Brooks, K. Bica-Schroder, C. Schroder;* Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether. Int. J. Mol. Sci. 2020, 21(17), 6222, (DOI: 10.3390/ijms21176222).
72. Y. M. Elbatrawi, K.P. Pedretty, N. Giddings, H. Lee Woodcock, J. R Del Valle;* δ-Azaproline and its oxidized variants. J. Org. Chem. 2020, (DOI: acs.joc.9b03384).
71. O. A. Pemberton, R. E. Noor, V. Kumar, R. Sanishvili, M. T. Kemp, F. L. Kearns, H. Lee Woodcock, Ioannis Gelis,*Y. Chen;* Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc. Nat. Acadm. Sci., 2020, (DOI: 10.1073/pnas.1922203117).
70. D. Wolfe, J. Persichetti, A. Sharma, P. S. Hudson, H. Lee Woodcock, E. O'Brien;* Hierarchical Markov State Model Building to Describe Molecular Processes, J. Chem. Theory. Comput., 2020, (DOI: acs.jctc.9b00955).
69. J. N. Kuhn, H. Lee Woodcock, M. A. Barakat, M. A. Alghamdi; Metal Chelating Composites, Methods of Using Composites, and Methods of Making Composites. U.S. patent number 10,343,143, July 2019.
68: P. S. Hudson, H. Lee Woodcock,* S. Boresch;* On the use of interaction energies in QM/MM free energy simulations. J. Chem. Theory Comput., 2019, 15, 4632-4645. (DOI: 10.1021/acs.jctc.9b00084).
67. F. L. Kearns, C. Robart, M. T. Kemp, S. L. Vankayala, B. M. Chapin, E. V. Anslyn, H. Lee Woodcock,* and J. D. Larkin;* Modeling Boronic Acid Based Flourescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid (DMPBA). J. Chem. Inf. Model., 2019, 59, 2150-2158. (DOI: 10.1021/acs.jcim.8b00987).
66. F. L. Kearns, L. Warrensford, S. Boresch,* H. Lee Woodcock;* The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations. Molecules, 2019, 24, 681. (DOI: 10.3390/molecules24040681).
65. P. S. Hudson, S. Boresch, D. M. Rogers,* H. Lee Woodcock;* Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching. J. Chem. Theory Comput., 2018, 14, 6327–6335. (DOI: 10.1021/acs.jctc.8b00517).
64. P. S. Hudson, K. Han, H. Lee Woodcock, B. R. Brooks; Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J Comput Aided Mol Des, 2018, 32, 983–999. (DOI: 10.1007/s10822-018-0165-3).
63. J. E. McGeehan,* G. T. Beckham,* H. Lee Woodcock;* Engineering a plastic-digesting enzyme: Understanding an enzyme which can digest some of our most commonly polluting plastic packaging. Baking Europe, Summer 2018, 54-56.
62. J. N. Kuhn, H. Lee Woodcock, M. A. Barakat, M. A. Alghamdi; Metal Chelating Composites, Methods of Using Composites, and Methods of Making Composites. U.S. patent number 9,950,307, 2018.
72. Y. M. Elbatrawi, K.P. Pedretty, N. Giddings, H. Lee Woodcock, J. R Del Valle;* δ-Azaproline and its oxidized variants. J. Org. Chem. 2020, (DOI: acs.joc.9b03384).
71. O. A. Pemberton, R. E. Noor, V. Kumar, R. Sanishvili, M. T. Kemp, F. L. Kearns, H. Lee Woodcock, Ioannis Gelis,*Y. Chen;* Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc. Nat. Acadm. Sci., 2020, (DOI: 10.1073/pnas.1922203117).
70. D. Wolfe, J. Persichetti, A. Sharma, P. S. Hudson, H. Lee Woodcock, E. O'Brien;* Hierarchical Markov State Model Building to Describe Molecular Processes, J. Chem. Theory. Comput., 2020, (DOI: acs.jctc.9b00955).
69. J. N. Kuhn, H. Lee Woodcock, M. A. Barakat, M. A. Alghamdi; Metal Chelating Composites, Methods of Using Composites, and Methods of Making Composites. U.S. patent number 10,343,143, July 2019.
68: P. S. Hudson, H. Lee Woodcock,* S. Boresch;* On the use of interaction energies in QM/MM free energy simulations. J. Chem. Theory Comput., 2019, 15, 4632-4645. (DOI: 10.1021/acs.jctc.9b00084).
67. F. L. Kearns, C. Robart, M. T. Kemp, S. L. Vankayala, B. M. Chapin, E. V. Anslyn, H. Lee Woodcock,* and J. D. Larkin;* Modeling Boronic Acid Based Flourescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid (DMPBA). J. Chem. Inf. Model., 2019, 59, 2150-2158. (DOI: 10.1021/acs.jcim.8b00987).
66. F. L. Kearns, L. Warrensford, S. Boresch,* H. Lee Woodcock;* The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations. Molecules, 2019, 24, 681. (DOI: 10.3390/molecules24040681).
65. P. S. Hudson, S. Boresch, D. M. Rogers,* H. Lee Woodcock;* Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching. J. Chem. Theory Comput., 2018, 14, 6327–6335. (DOI: 10.1021/acs.jctc.8b00517).
64. P. S. Hudson, K. Han, H. Lee Woodcock, B. R. Brooks; Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J Comput Aided Mol Des, 2018, 32, 983–999. (DOI: 10.1007/s10822-018-0165-3).
63. J. E. McGeehan,* G. T. Beckham,* H. Lee Woodcock;* Engineering a plastic-digesting enzyme: Understanding an enzyme which can digest some of our most commonly polluting plastic packaging. Baking Europe, Summer 2018, 54-56.
62. J. N. Kuhn, H. Lee Woodcock, M. A. Barakat, M. A. Alghamdi; Metal Chelating Composites, Methods of Using Composites, and Methods of Making Composites. U.S. patent number 9,950,307, 2018.
60. B. Fritch, A. Kosolapov, P. S. Hudson, D. Nissley, H. Lee Woodcock, C. Deutsch,* E. O'Brien;* Origins of the mechanochemical coupling of peptide bond formation to protein synthesis. J. Am. Chem. Soc., 2018, 140, 5077–5087 (DOI: 10.1021/jacs.7b11044).
59. S. Handa, D. R. Dempsey, D. Ramamoorthy, N. Cook, W. C. Guida, T. J. Spradling, J. K. White, H Lee Woodcock, D. J. Merkler;* Mechanistic Studies of 1-Deoxy-D-Xylulose-5-Phosphate Synthase from Deinococcus radiodurans. Biochem Mol Biol J., 2018; 4, 1-11 (DOI: 10.21767/2471-8084.100051).
58. M. P. Sarnowski, K. P. Pedretty, N. Giddings, H. Lee Woodcock, J. R. Del Valle;. Synthesis and β-sheet propensity of constrained N-amino peptides. Bioorg. Med. Chem., 2017; 26, 1162-1166 (DOI: 10.1016/j.bmc.2017.08.017).
57. B. M. Chapin, P. Metola, S. L. Vankayala, H. Lee Woodcock, T. J. Mooibroek, V. M. Lynch, J. D. Larkin,* and E. V. Anslyn;* Disaggregation is a Mechanism for Emission Turn-On of ortho-Aminomethylphenylboronic Acid-Based Saccharide Sensors. J. Am. Chem. Soc., 2017; 139, 5568-5578 (DOI: 10.1021/jacs.7b01755).
56. F. L. Kearns, P. S. Hudson, H. Lee Woodcock,* S. Boresch;* Computing converged free energy differences between levels of theory via non-equilibrium work. J. Comput. Chem., 2017; 38, 1376-1388 (DOI: 10.1002/jcc.24706).
55. S. Boresch,* H. Lee Woodcock;* Convergence of single-step free energy perturbation. Mol. Phys., 2017; 115, 1200-1213 (DOI: 10.1080/00268976.2016.1269960).
54. S. L. Vankayalaa, F. L. Kearns, B. J. Baker, J. D. Larkin, H. Lee Woodcock;* Elucidating a chemical defense mechanism of Antarctic sponges: A computational study. J. Mol. Graph. Model., 2017; 71, 104-115 (DOI: 10.1016/j.jmgm.2016.11.004).
53. J. K. White, S. Handa, S. L. Vankayala, D. J. Merkler, H. L. Woodcock;* Thiamin Diphosphate Activation in 1-deoxy-D-xylulose 5-Phosphate Synthase: Insights into the Mechanism and Underlying Intermolecular Interactions. J. Phys. Chem. B, 2016; 120, 9922–9934 (DOI: 10.1021/acs.jpcb.6b07248).
52. F. L Kearns, P. S. Hudson, S. Boresch, H. L. Woodcock;* Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis. Methods in Enzymology, 2016; 577, 75–104 (10.1016/bs.mie.2016.05.053).
51. A. S. Mhashilkar; S. L. Vankayala; C. Liu; F. Kearns; P. Mehrotra; G. Tzertzinis; S. R. Palli; H. L. Woodcock; T. R. Unnasch;* Identification of ecdysone hormone receptor agonists as a therapeutic approach for treating filarial infections. PLOS Neglected Tropical Diseases, 2016; 10(6), e0004772.
50. G. A. Hunter, S. L. Vankayalab, M. E. Gillama, F. L. Kearns, H. L. Woodcock,* and G. C. Ferreira;* The conserved active site histidine-glutamate pair of ferrochelatase coordinately catalyzes porphyrin metalation. J. Porphyrins Phthalocyanines, 2016; 20, 556–569 (DOI: 10.1142/S1088424616500395).
49. G. Konig, Y. Mei, F. Pickard, A. Simmonett, B. T. Miller, J. Herbert, H. L. Woodcock, B. R. Brooks, Y. Shao;* Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Method J. Chem. Theory Comput., 2016 12(1), 332-344. (DOI: 10.1021/acs.jctc.5b00874).
48. P. S. Hudson, H. L. Woodcock,* S. Boresch;* Use of Non-equilibrium Work Methods to Compute Free Energy Differences between MM and QM Representations of Molecular Systems. J. Phys. Chem. Lett., 2015; 6(23), 4850–4856. (DOI: 10.1021/acs.jpclett.5b02164).
47. J. Konc BT Miller, T Stular, S. Lesnik, H. L. Woodcock, BR Brooks, D. Janezic;* ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model., 2015; 55(11), 2308−2314. (DOI: 10.1021/acs.jcim.5b00534).
46. D. Nichols, J. C. Hargis, R. Sanishvili, P. Jaishankar, K. DeFrees, E. Smith, K. Wang, F. Prati, A. Renslo, H. L. Woodcock, Y. Chen;* Ligand-induced proton transfer and low-barrier hydrogen bond revealed by X-ray crystallography. J. Am. Chem. Soc., 2015; 137(25), 8086–8095. (DOI: 10.1021/jacs.5b00749).
45. Y. Shao, Z. Gan, E. Epifanovsky, A. T. B. Gilbert, M. Wormit, J. Kussmann, A. W. Lange, A. Behn, J. Deng, X. Feng, D. Ghosh, M. Goldey, P. R. Horn, L. D. Jacobson, I. Kaliman, R. Z. Khaliullin, T. Kus, A. Landau, J. Liu, E. I. Proynov, Y. M. Rhee, R. M. Richard, M. A. Rohrdanz, R. P. Steele, E. J. Sundstrom, H. L. Woodcock III, P. M. Zimmerman, D. Zuev, B. Albrecht, E. Alguire, B. Austin, G. J. O. Beran, Y. A. Bernard, E. Berquist, K. Brandhorst, K. B. Bravaya, S. T. Brown, D. Casanova, C.-M. Chang, Y. Chen, S. H. Chien, K. D. Closser, D. L. Crittenden, M. Diedenhofen, R. A. DiStasio Jr., H. Dop, A. D. Dutoi, R. G. Edgar, S. Fatehi, L. Fusti-Molnar, A. Ghysels, A. Golubeva-Zadorozhnaya, J. Gomes, M. W. D. Hanson-Heine, P. H. P. Harbach, A. W. Hauser, E. G. Hohenstein, Z. C. Holden, T.-C. Jagau, H. Ji, B. Kaduk, K. Khistyaev, J. Kim, J. Kim, R. A. King, P. Klunzinger, D. Kosenkov, T. Kowalczyk, C. M. Krauter, K. U. Lao, A. Laurent, K. V. Lawler, S. V. Levchenko, C. Y. Lin, F. Liu, E. Livshits, R. C. Lochan, A. Luenser, P. Manohar, S. F. Manzer, S.-P. Mao, N. Mardirossian, A. V. Marenich, S. A. Maurer, N. J. Mayhall, C. M. Oana, R. Olivares-Amaya, D. P. O'Neill, J. A. Parkhill, T. M. Perrine, R. Peverati, P. A. Pieniazek, A. Prociuk, D. R. Rehn, E. Rosta, N. J. Russ, N. Sergueev, S. M. Sharada, S. Sharmaa, D. W. Small, A. Sodt, T. Stein, D. Stuck, Y.-C. Su, A. J. W. Thom, T. Tsuchimochi, L. Vogt, O. Vydrov, T. Wang, M. A. Watson, J. Wenzel, A. White, C. F. Williams, V. Vanovschi, S. Yeganeh, S. R. Yost, Z.-Q. You, I. Y. Zhang, X. Zhang, Y. Zhou, B. R. Brooks, G. K. L. Chan, D. M. Chipman, C. J. Cramer, W. A. Goddard III, M. S. Gordon, W. J. Hehre, A. Klamt, H. F. Schaefer III, M. W. Schmidt, C. D. Sherrill, D. G. Truhlar, A. Warshel, X. Xua, A. Aspuru-Guzik R. Baer, A. T. Bell, N. A. Besley, J.-D. Chai, A. Dreuw, B. D. Dunietz, T. R. Furlani, S. R. Gwaltney, C.-P. Hsu, Y. Jung, J. Kong, D. S. Lambrecht, W. Liang, C. Ochsenfeld, V. A. Rassolov, L. V. Slipchenko, J. E. Subotnik, T. Van Voorhis, J. M. Herbert, A. I. Krylov, P. M. W. Gill, M. Head-Gordon. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol. Phys., 2015; 113(2), 184-215. (DOI: 10.1080/00268976.2014.952696).
44. R. W. Larsen*, A. Karolak, T. A. Word, M. T. Kemp, C. L. Whittington, H. L. Woodcock, A. van der Vaart; Photoacoustic calorimtery study of ligand photorelease from Ru(II)bis(2,2’-bipyridine)(6,6’-dimethyl-2,2’-bipyridine) complexes in aqueous solution. Chem. Phys. Lett., 2015; 619, 214-218. (DOI: 10.1016/j.cplett.2014.11.012).
43. I. Weidlich, Y. Pevzner, B. T. Miller, I. Filippov, H. L. Woodcock, B. R. Brooks; Development and implementation of (Q)SAR modeling within the CHARMMing Web-user interface. J. Comput. Chem., 2015; 36(1), 62–67 (PMID: 25362883, DOI: 10.1002/jcc.23765).
42. P. S. Hudson, J. K. White, F. L. Kearns, M. Hodoscek, S. Boresch, H. L. Woodcock*; Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes. Biochim. Biophys. Acta, 2015; 1850(5), 944-953. (PMID: 25239198, DOI: 10.1016/j.bbagen.2014.09.016).
41. Y. Pevzner, E. Frugier, V. Schalk, A. Caflisch, H. L. Woodcock*; Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design. J. Chem. Inf. Mod., 2014; 54 (9), 2612–2620.
40. B. S. Perrin, B. T. Miller, V. Schalk, H. L. Woodcock, B. R. Brooks, T. Ichiye; Web-based computational chemistry lessons in CHARMMing III: Reduction potentials of electron transfer proteins. PLOS Comput. Biol., 2014; 10: e1003739.
39. F. C. Pickard, B. T. Miller, V. Schalk, M. G. Lerner, H. L. Woodcock, B. R. Brooks; Web based computational chemistry education with CHARMMing II: Coarse Grained Protein Folding. PLOS Comput. Biol., 2014; 10: e1003738.
38. B. T. Miller, R. P. Singh, V. Schalk, Y. Pevzner, J. Sun, C. S. Miller, S. Boresch, T. Ichiye, B. R. Brooks, H. L. Woodcock*, Web based computational chemistry education with CHARMMing I: Lessons and Tutorial. PLOS Comput. Biol., 2014; 10: e1003719.
37. Y. Pevzner, D. N. Santiago, J. S. Fries, R. S. Metcalf, K. G. Daniel, L. Calcul, H. L. Woodcock, B. J. Baker, W. C. Guida, W. H. Brooks; Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery. AIMS Molec. Sci., 2014; 1(2), 81-98.
36. J. C. Hargis, J. K. White, Y. Chen, H. L. Woodcock*; Can Molecular Dynamics and QM/MM solve the Penicillin Binding Protein Protonation Puzzle?. J. Chem. Inf. Mod., 2014; 54(5), 1412–1424.
35. G. Konig, P. S. Hudson, S. Boresch,* H. L. Woodcock*; Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes. J. Chem. Theory Comput., 2014; 10(4), 1406–1419.
34. J. C. Hargis, S. L. Vankayala, J. K. White, H. L. Woodcock*; Identification and characterization of non-covalent interactions that drive binding and specificity in DD-peptidases and β-lactamases. J. Chem. Theory Comput., 2014; 20(2), 855-864.
33. S. L. Vankayala, J. C. Hargis, H. L. Woodcock;* How Does Catalase Release Nitric Oxide? A Computational Structure Activity Relationship Study. J. Chem. Inf. Mod., 2013; 53(11), 2591-2961.
32. R. Kumar, M. A. Barakat, Y. A. Daza, H. L. Woodcock, J. N. Kuhn; EDTA functionalized silica for removal of Cu(II), Zn(II) and Ni(II) from aqueous solution. J. Colloid Interface Sci., 2013; 408; 200-205.
31. M. H. Ramadan, M. A. Barakat, J. N. Kuhn, H. L. Woodcock; Equilibrium and Kinetics of Pb2+ removal from aqueous solution by dendrimer/titania composites. Desalination and Water Treatment, 2013; 1(1), 1-7 (DOI: 10.1080/19443994.2013.815584).
30. V. A. Castillo, V.A. M. A. Barakat, M. H. Ramadan, H. L. Woodcock, J. N. Kuhn; Metal Ion Remediation by Polyamidoamine Dendrimers: A Comparison of Metal Ion, Oxidation State, and Titania Immobilization. Int. J. Environ. Sci. Tech., 2013; DOI: 10.1007/s13762-013-0346-5.
29. M. A. Barakat, M.H. Ramadan, M.A. Al-Ghamdi, S. S. Al-Garny, H. L. Woodcock, J.N. Kuhn; Remediation of Cu(II), Ni(II), and Cr(III) ions from simulated wastewater by dendrimer/titania composites. J Environ Manage, 2013; 117; 50-57.
28. D. N. Santiago, Y. Pevzner, A. A. Durand, M. P. Tran, R. R. Scheerer, K. Daniel, S. S. Sung, H. L. Woodcock, W. C. Guida, W. H. Brooks; Validation of Virtual Target Screening. J. Chem. Inf. Mod., 2012; 52(8); 2192-2203.
27. S. L. Vankayala, J. C. Hargis, H. L. Woodcock*; Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors. J. Chem. Inf. Mod., 2012; 52(5); 1288-1297.
26. C. L. Whittington, W. A. Maza, H. L. Woodcock,* R. W. Larsen*; Understanding Ion Sensing in Zn(II) Porphyrins: Spectroscopic and Computational Studies of Nitrite/Nitrate Binding. Inorg. Chem., 2012; 51(8); 4756-4762.
25. M. R. Mankbadi, M. A. Barakat, M. H. Ramadan, H. L. Woodcock, J. N. Kuhn*; Iron chelation by polyamidoamine dendrimers: a second-order kinetic model for metal-amine complexation. J. Chem. Phys. B., 2011; 115(46); 13534-13540.
24. J. L. Belof, C. R. Cioce, X. Xu, X. P. Zhang, B. Space, H. L. Woodcock*; Characterization of Tunable Radical Metal-Carbenes: Key Intermediates in Catalytic Cyclopropanation. Organometallics, 2011; 30(10); 2739-2746.
23. S. E. Larson, G. L. Li, G. B. Rowland, D. Junge, R. C. Huang, H. L. Woodcock, J. C. Antilla; Catalytic Asymmetric Aza-Darzens Reaction with a Vaulted Biphenanthrol Magnesium Phosphate Salt. Org. Lett., 2011; 13(9); 2188-2191.
22. H. L. Woodcock,* B. T. Miller, M. Hodoscek, A. Okur, J. D. Larkin, B. R. Brooks*; MSCALE: A General Utility for Multiscale Modeling. J. Chem. Theory Comput., 2011; 7(4); 1208-1219. (Top 10 Most Read 2011)
21. J. C. Hargis, E. Voehringer-Martinez, H. L. Woodcock, A. Toro-Labbe, H. F. Schaefer; Characterizing the Mechanism of the Double Proton Transfer in the Formamide Dimer. J. Phys. Chem. A, 2011; 115(12); 2650-2657.
20. A. Ghysels,* H. L. Woodcock,* J. D. Larkin, B. T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroek, M. Waroquier, and B. R. Brooks; Efficient calculation of QM/MM frequencies with the Mobile Block Hessian. J. Chem. Theory. Comput., 2011; 7(2); 496-514.
19. E. Rosta, H. L. Woodcock B. R. Brooks, G. Hummer; Artificial reaction coordinate "tunneling" in free energy calculations: the catalytic reaction of RNase H. J. Comp. Chem.; 2009; 30 (11); 1634-1641.
18. B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, L. Caves, Q. Cui, A. Dinner, S. Fischer, J. Gao, M. Hodoscek, K. Kuczera, T. Lazaridis, J. Ma, E. Paci, R. W. Pastor, C. B. Post, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu and M. Karplus; CHARMM The Biomolecular Simulation Program. J. Comp. Chem.; 2009; 30 (10); 1545-1614.
17. H. Lee Woodcock, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B. R. Brooks; Vibrational Subsystem Analysis: A Method for Probing Free Energies and Correlations in the Harmonic Limit. J. Chem. Phys.; 2008; 129; 214109.
16. B. T. Miller, R. P. Singh, J. B. Klauda, M. Hodoscek, B. R. Brooks, and H. Lee Woodcock* CHARMMing: A New, Flexible, Web-based front-end to CHARMM. J. Chem. Inf. Mod.; 2008; 48(9); 1920-1929.
15. H. Lee Woodcock, B. R. Brooks, R. W. Pastor; Pathways and populations: Stereo-electronic insights into the exocyclic torsion of 5-hydroxy-methyl-tetrahydropyran. J. Am. Chem. Soc.; 2008; 130(20); 6345-6347.
14. N. H. Martin, R. M. Floyd, H. Lee Woodcock and S. Huffman; Computation of Through- Space NMR Shielding Effects in Aromatic Ring π-Stacked Complexes. J. Mol. Graphics Mod.; 2008; 26(7); 1125-1130.
13. H. Lee Woodcock, Milan Hodosceck, B. R. Brooks; Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms; J. Phys. Chem. A; 2007; 111(26); 5720-5728.
12. H. Lee Woodcock, R. W. Pastor, A. D. MacKerell, B. R. Brooks; Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate : 2-Ethoxy Tetrahydropyran. Biophys. J.; 2007; 93(1); 1-10.
11. H. Lee Woodcock, Damian Moran, Paul v.R. Schleyer, H.F. Schaefer; Carbene Stabilization by Aryl Substitudents. Is Bigger Better? J. Am. Chem. Soc.; 2007; 129(12); 3763-3770.
10. H. Lee Woodcock, Milan Hodosceck, Andrew T.B. Gilbert, Peter M.W. Gill, H.F. Schaefer, Bernard R. Brooks; Interfacing CHARMM and Q-Chem to perform QM/MM and QM/MM reaction pathway calculations. J. Comp. Chem.; 2007; 28(9); 1485-1502.
9. Y. Shao, L. Fusti-Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. T. Brown, A. T. B. Gilbert, L. V. lipchenko, S. V. Levchenko, D. P. ONeill, R. A. Distasio, R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley, J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele, V. A. Rassolov, P. E. Maslen, P. P. Korambath, R. D. Adamson, B. Austin, J. Baker, E. F. C. Byrd, H. Daschel, R. J. Doerksen, A. Dreuw, B. D. Dunietz, A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C. P. Hsu, G. Kedziora, R. Z. Khalliulin, P. Klunzinger, A. M. Lee, M. S. Lee, W. Liang, I. Lotan, N. Nair, B. Peters, E. I. Proynov, P. A. Pieniazek, Y. M. Rhee, J. Ritchie, E. Rosta, D. C. Sherrill, A. C. Simmonett, J. E. Subotnik, H. Lee Woodcock, W. Zhang, A. T. Bell, A. K. Chakraborty, D. M. Chipman, F. J. Keil, A. Warshel, W. J. Hehre, H. F. Schaefer, J. Kong, A. I. Krylov, P. M. W. Gill, M. Head-Gordon; Advances in methods and algorithms in a modern quantum chemistry program package. (Phys. Chem. Chem. Phys.); 2006; 8; 3172-3191.
8. Speakman LD, Papas BN, H. Lee Woodcock, Schaefer HF; A reinterpretation of microwave and infrared spectroscopic studies of benzaldehyde; J. Chem. Phys.; 2004; 120 (9); 4247-4250.
7. Papas BN, Wang SY, DeYonker NJ, H. Lee Woodcock, Schaefer HF; Naphthalenyl, anthracenyl, tetracenyl, and pentacenyl radicals and their anions; J. Phys. Chem. A; 2003; 107 (32); 6311-6316.
6. Moran D, H. Lee Woodcock, Chen ZF, Schaefer HF, Schleyer PvR; The viability of small endohedral hydrocarbon cage complexes: X@C4H4, X@C8H8, X@C8H14, X@C10H16, X@C12H12, and X@C16H16; J. Am. Chem. Soc.; 2003; 125 (37); 11442-11451.
5. H. Lee Woodcock, Milan Hodoscek, Paul Sherwood, Yong S. Lee, Henry F. Schaefer III, and Bernard R. Brooks; Exploring the QM/MM Replica Path Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate; Theor. Chem. Acc. 2003; 109(3); 140-148.
4. H. Lee Woodcock, H.F. Schaefer, P.R. Schreiner; Problematic energy differences between cumulenes and poly-ynes: Does this point to a systematic improvement of density functional theory? J. Phys. Chem. A 2002; 106(49) 11923-11931.
3. Ned H. Martin, Justin D. Brown, Kimberly H. Nance, Henry F. Schaefer III, Paul v. R. Schleyer, Zhi-Xiang Wang, and H. Lee Woodcock; Analysis of the Origin of Through-Space NMR (De)shielding by Selected Organic Functional Groups; Org. Lett.;2001; 3(24); 3823.
2. H. Lee Woodcock, Steven S. Wesolowski, Yukio Yamaguchi, and H.F. Schaefer; Systematic Study of the Neutral Radical PH2; J. Chem. Phys. 2001; 105(20); 5037.
1. H. Lee Woodcock, Damian Moran, Paul von Rague Schleyer and H.F. Schaefer; The Almost Bottleable Triplet Carbene: 2,6-dibromo-4-tert-butyl-2',6'-bistrifluoromethyl-4'-isopropyldiphenylcarbene; J. Am. Chem. Soc.; 2001; 123(18); 4331.
59. S. Handa, D. R. Dempsey, D. Ramamoorthy, N. Cook, W. C. Guida, T. J. Spradling, J. K. White, H Lee Woodcock, D. J. Merkler;* Mechanistic Studies of 1-Deoxy-D-Xylulose-5-Phosphate Synthase from Deinococcus radiodurans. Biochem Mol Biol J., 2018; 4, 1-11 (DOI: 10.21767/2471-8084.100051).
58. M. P. Sarnowski, K. P. Pedretty, N. Giddings, H. Lee Woodcock, J. R. Del Valle;. Synthesis and β-sheet propensity of constrained N-amino peptides. Bioorg. Med. Chem., 2017; 26, 1162-1166 (DOI: 10.1016/j.bmc.2017.08.017).
57. B. M. Chapin, P. Metola, S. L. Vankayala, H. Lee Woodcock, T. J. Mooibroek, V. M. Lynch, J. D. Larkin,* and E. V. Anslyn;* Disaggregation is a Mechanism for Emission Turn-On of ortho-Aminomethylphenylboronic Acid-Based Saccharide Sensors. J. Am. Chem. Soc., 2017; 139, 5568-5578 (DOI: 10.1021/jacs.7b01755).
56. F. L. Kearns, P. S. Hudson, H. Lee Woodcock,* S. Boresch;* Computing converged free energy differences between levels of theory via non-equilibrium work. J. Comput. Chem., 2017; 38, 1376-1388 (DOI: 10.1002/jcc.24706).
55. S. Boresch,* H. Lee Woodcock;* Convergence of single-step free energy perturbation. Mol. Phys., 2017; 115, 1200-1213 (DOI: 10.1080/00268976.2016.1269960).
54. S. L. Vankayalaa, F. L. Kearns, B. J. Baker, J. D. Larkin, H. Lee Woodcock;* Elucidating a chemical defense mechanism of Antarctic sponges: A computational study. J. Mol. Graph. Model., 2017; 71, 104-115 (DOI: 10.1016/j.jmgm.2016.11.004).
53. J. K. White, S. Handa, S. L. Vankayala, D. J. Merkler, H. L. Woodcock;* Thiamin Diphosphate Activation in 1-deoxy-D-xylulose 5-Phosphate Synthase: Insights into the Mechanism and Underlying Intermolecular Interactions. J. Phys. Chem. B, 2016; 120, 9922–9934 (DOI: 10.1021/acs.jpcb.6b07248).
52. F. L Kearns, P. S. Hudson, S. Boresch, H. L. Woodcock;* Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis. Methods in Enzymology, 2016; 577, 75–104 (10.1016/bs.mie.2016.05.053).
51. A. S. Mhashilkar; S. L. Vankayala; C. Liu; F. Kearns; P. Mehrotra; G. Tzertzinis; S. R. Palli; H. L. Woodcock; T. R. Unnasch;* Identification of ecdysone hormone receptor agonists as a therapeutic approach for treating filarial infections. PLOS Neglected Tropical Diseases, 2016; 10(6), e0004772.
50. G. A. Hunter, S. L. Vankayalab, M. E. Gillama, F. L. Kearns, H. L. Woodcock,* and G. C. Ferreira;* The conserved active site histidine-glutamate pair of ferrochelatase coordinately catalyzes porphyrin metalation. J. Porphyrins Phthalocyanines, 2016; 20, 556–569 (DOI: 10.1142/S1088424616500395).
49. G. Konig, Y. Mei, F. Pickard, A. Simmonett, B. T. Miller, J. Herbert, H. L. Woodcock, B. R. Brooks, Y. Shao;* Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Method J. Chem. Theory Comput., 2016 12(1), 332-344. (DOI: 10.1021/acs.jctc.5b00874).
48. P. S. Hudson, H. L. Woodcock,* S. Boresch;* Use of Non-equilibrium Work Methods to Compute Free Energy Differences between MM and QM Representations of Molecular Systems. J. Phys. Chem. Lett., 2015; 6(23), 4850–4856. (DOI: 10.1021/acs.jpclett.5b02164).
47. J. Konc BT Miller, T Stular, S. Lesnik, H. L. Woodcock, BR Brooks, D. Janezic;* ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model., 2015; 55(11), 2308−2314. (DOI: 10.1021/acs.jcim.5b00534).
46. D. Nichols, J. C. Hargis, R. Sanishvili, P. Jaishankar, K. DeFrees, E. Smith, K. Wang, F. Prati, A. Renslo, H. L. Woodcock, Y. Chen;* Ligand-induced proton transfer and low-barrier hydrogen bond revealed by X-ray crystallography. J. Am. Chem. Soc., 2015; 137(25), 8086–8095. (DOI: 10.1021/jacs.5b00749).
45. Y. Shao, Z. Gan, E. Epifanovsky, A. T. B. Gilbert, M. Wormit, J. Kussmann, A. W. Lange, A. Behn, J. Deng, X. Feng, D. Ghosh, M. Goldey, P. R. Horn, L. D. Jacobson, I. Kaliman, R. Z. Khaliullin, T. Kus, A. Landau, J. Liu, E. I. Proynov, Y. M. Rhee, R. M. Richard, M. A. Rohrdanz, R. P. Steele, E. J. Sundstrom, H. L. Woodcock III, P. M. Zimmerman, D. Zuev, B. Albrecht, E. Alguire, B. Austin, G. J. O. Beran, Y. A. Bernard, E. Berquist, K. Brandhorst, K. B. Bravaya, S. T. Brown, D. Casanova, C.-M. Chang, Y. Chen, S. H. Chien, K. D. Closser, D. L. Crittenden, M. Diedenhofen, R. A. DiStasio Jr., H. Dop, A. D. Dutoi, R. G. Edgar, S. Fatehi, L. Fusti-Molnar, A. Ghysels, A. Golubeva-Zadorozhnaya, J. Gomes, M. W. D. Hanson-Heine, P. H. P. Harbach, A. W. Hauser, E. G. Hohenstein, Z. C. Holden, T.-C. Jagau, H. Ji, B. Kaduk, K. Khistyaev, J. Kim, J. Kim, R. A. King, P. Klunzinger, D. Kosenkov, T. Kowalczyk, C. M. Krauter, K. U. Lao, A. Laurent, K. V. Lawler, S. V. Levchenko, C. Y. Lin, F. Liu, E. Livshits, R. C. Lochan, A. Luenser, P. Manohar, S. F. Manzer, S.-P. Mao, N. Mardirossian, A. V. Marenich, S. A. Maurer, N. J. Mayhall, C. M. Oana, R. Olivares-Amaya, D. P. O'Neill, J. A. Parkhill, T. M. Perrine, R. Peverati, P. A. Pieniazek, A. Prociuk, D. R. Rehn, E. Rosta, N. J. Russ, N. Sergueev, S. M. Sharada, S. Sharmaa, D. W. Small, A. Sodt, T. Stein, D. Stuck, Y.-C. Su, A. J. W. Thom, T. Tsuchimochi, L. Vogt, O. Vydrov, T. Wang, M. A. Watson, J. Wenzel, A. White, C. F. Williams, V. Vanovschi, S. Yeganeh, S. R. Yost, Z.-Q. You, I. Y. Zhang, X. Zhang, Y. Zhou, B. R. Brooks, G. K. L. Chan, D. M. Chipman, C. J. Cramer, W. A. Goddard III, M. S. Gordon, W. J. Hehre, A. Klamt, H. F. Schaefer III, M. W. Schmidt, C. D. Sherrill, D. G. Truhlar, A. Warshel, X. Xua, A. Aspuru-Guzik R. Baer, A. T. Bell, N. A. Besley, J.-D. Chai, A. Dreuw, B. D. Dunietz, T. R. Furlani, S. R. Gwaltney, C.-P. Hsu, Y. Jung, J. Kong, D. S. Lambrecht, W. Liang, C. Ochsenfeld, V. A. Rassolov, L. V. Slipchenko, J. E. Subotnik, T. Van Voorhis, J. M. Herbert, A. I. Krylov, P. M. W. Gill, M. Head-Gordon. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol. Phys., 2015; 113(2), 184-215. (DOI: 10.1080/00268976.2014.952696).
44. R. W. Larsen*, A. Karolak, T. A. Word, M. T. Kemp, C. L. Whittington, H. L. Woodcock, A. van der Vaart; Photoacoustic calorimtery study of ligand photorelease from Ru(II)bis(2,2’-bipyridine)(6,6’-dimethyl-2,2’-bipyridine) complexes in aqueous solution. Chem. Phys. Lett., 2015; 619, 214-218. (DOI: 10.1016/j.cplett.2014.11.012).
43. I. Weidlich, Y. Pevzner, B. T. Miller, I. Filippov, H. L. Woodcock, B. R. Brooks; Development and implementation of (Q)SAR modeling within the CHARMMing Web-user interface. J. Comput. Chem., 2015; 36(1), 62–67 (PMID: 25362883, DOI: 10.1002/jcc.23765).
42. P. S. Hudson, J. K. White, F. L. Kearns, M. Hodoscek, S. Boresch, H. L. Woodcock*; Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes. Biochim. Biophys. Acta, 2015; 1850(5), 944-953. (PMID: 25239198, DOI: 10.1016/j.bbagen.2014.09.016).
41. Y. Pevzner, E. Frugier, V. Schalk, A. Caflisch, H. L. Woodcock*; Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design. J. Chem. Inf. Mod., 2014; 54 (9), 2612–2620.
40. B. S. Perrin, B. T. Miller, V. Schalk, H. L. Woodcock, B. R. Brooks, T. Ichiye; Web-based computational chemistry lessons in CHARMMing III: Reduction potentials of electron transfer proteins. PLOS Comput. Biol., 2014; 10: e1003739.
39. F. C. Pickard, B. T. Miller, V. Schalk, M. G. Lerner, H. L. Woodcock, B. R. Brooks; Web based computational chemistry education with CHARMMing II: Coarse Grained Protein Folding. PLOS Comput. Biol., 2014; 10: e1003738.
38. B. T. Miller, R. P. Singh, V. Schalk, Y. Pevzner, J. Sun, C. S. Miller, S. Boresch, T. Ichiye, B. R. Brooks, H. L. Woodcock*, Web based computational chemistry education with CHARMMing I: Lessons and Tutorial. PLOS Comput. Biol., 2014; 10: e1003719.
37. Y. Pevzner, D. N. Santiago, J. S. Fries, R. S. Metcalf, K. G. Daniel, L. Calcul, H. L. Woodcock, B. J. Baker, W. C. Guida, W. H. Brooks; Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery. AIMS Molec. Sci., 2014; 1(2), 81-98.
36. J. C. Hargis, J. K. White, Y. Chen, H. L. Woodcock*; Can Molecular Dynamics and QM/MM solve the Penicillin Binding Protein Protonation Puzzle?. J. Chem. Inf. Mod., 2014; 54(5), 1412–1424.
35. G. Konig, P. S. Hudson, S. Boresch,* H. L. Woodcock*; Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes. J. Chem. Theory Comput., 2014; 10(4), 1406–1419.
34. J. C. Hargis, S. L. Vankayala, J. K. White, H. L. Woodcock*; Identification and characterization of non-covalent interactions that drive binding and specificity in DD-peptidases and β-lactamases. J. Chem. Theory Comput., 2014; 20(2), 855-864.
33. S. L. Vankayala, J. C. Hargis, H. L. Woodcock;* How Does Catalase Release Nitric Oxide? A Computational Structure Activity Relationship Study. J. Chem. Inf. Mod., 2013; 53(11), 2591-2961.
32. R. Kumar, M. A. Barakat, Y. A. Daza, H. L. Woodcock, J. N. Kuhn; EDTA functionalized silica for removal of Cu(II), Zn(II) and Ni(II) from aqueous solution. J. Colloid Interface Sci., 2013; 408; 200-205.
31. M. H. Ramadan, M. A. Barakat, J. N. Kuhn, H. L. Woodcock; Equilibrium and Kinetics of Pb2+ removal from aqueous solution by dendrimer/titania composites. Desalination and Water Treatment, 2013; 1(1), 1-7 (DOI: 10.1080/19443994.2013.815584).
30. V. A. Castillo, V.A. M. A. Barakat, M. H. Ramadan, H. L. Woodcock, J. N. Kuhn; Metal Ion Remediation by Polyamidoamine Dendrimers: A Comparison of Metal Ion, Oxidation State, and Titania Immobilization. Int. J. Environ. Sci. Tech., 2013; DOI: 10.1007/s13762-013-0346-5.
29. M. A. Barakat, M.H. Ramadan, M.A. Al-Ghamdi, S. S. Al-Garny, H. L. Woodcock, J.N. Kuhn; Remediation of Cu(II), Ni(II), and Cr(III) ions from simulated wastewater by dendrimer/titania composites. J Environ Manage, 2013; 117; 50-57.
28. D. N. Santiago, Y. Pevzner, A. A. Durand, M. P. Tran, R. R. Scheerer, K. Daniel, S. S. Sung, H. L. Woodcock, W. C. Guida, W. H. Brooks; Validation of Virtual Target Screening. J. Chem. Inf. Mod., 2012; 52(8); 2192-2203.
27. S. L. Vankayala, J. C. Hargis, H. L. Woodcock*; Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors. J. Chem. Inf. Mod., 2012; 52(5); 1288-1297.
26. C. L. Whittington, W. A. Maza, H. L. Woodcock,* R. W. Larsen*; Understanding Ion Sensing in Zn(II) Porphyrins: Spectroscopic and Computational Studies of Nitrite/Nitrate Binding. Inorg. Chem., 2012; 51(8); 4756-4762.
25. M. R. Mankbadi, M. A. Barakat, M. H. Ramadan, H. L. Woodcock, J. N. Kuhn*; Iron chelation by polyamidoamine dendrimers: a second-order kinetic model for metal-amine complexation. J. Chem. Phys. B., 2011; 115(46); 13534-13540.
24. J. L. Belof, C. R. Cioce, X. Xu, X. P. Zhang, B. Space, H. L. Woodcock*; Characterization of Tunable Radical Metal-Carbenes: Key Intermediates in Catalytic Cyclopropanation. Organometallics, 2011; 30(10); 2739-2746.
23. S. E. Larson, G. L. Li, G. B. Rowland, D. Junge, R. C. Huang, H. L. Woodcock, J. C. Antilla; Catalytic Asymmetric Aza-Darzens Reaction with a Vaulted Biphenanthrol Magnesium Phosphate Salt. Org. Lett., 2011; 13(9); 2188-2191.
22. H. L. Woodcock,* B. T. Miller, M. Hodoscek, A. Okur, J. D. Larkin, B. R. Brooks*; MSCALE: A General Utility for Multiscale Modeling. J. Chem. Theory Comput., 2011; 7(4); 1208-1219. (Top 10 Most Read 2011)
21. J. C. Hargis, E. Voehringer-Martinez, H. L. Woodcock, A. Toro-Labbe, H. F. Schaefer; Characterizing the Mechanism of the Double Proton Transfer in the Formamide Dimer. J. Phys. Chem. A, 2011; 115(12); 2650-2657.
20. A. Ghysels,* H. L. Woodcock,* J. D. Larkin, B. T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroek, M. Waroquier, and B. R. Brooks; Efficient calculation of QM/MM frequencies with the Mobile Block Hessian. J. Chem. Theory. Comput., 2011; 7(2); 496-514.
19. E. Rosta, H. L. Woodcock B. R. Brooks, G. Hummer; Artificial reaction coordinate "tunneling" in free energy calculations: the catalytic reaction of RNase H. J. Comp. Chem.; 2009; 30 (11); 1634-1641.
18. B. R. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, L. Caves, Q. Cui, A. Dinner, S. Fischer, J. Gao, M. Hodoscek, K. Kuczera, T. Lazaridis, J. Ma, E. Paci, R. W. Pastor, C. B. Post, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu and M. Karplus; CHARMM The Biomolecular Simulation Program. J. Comp. Chem.; 2009; 30 (10); 1545-1614.
17. H. Lee Woodcock, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B. R. Brooks; Vibrational Subsystem Analysis: A Method for Probing Free Energies and Correlations in the Harmonic Limit. J. Chem. Phys.; 2008; 129; 214109.
16. B. T. Miller, R. P. Singh, J. B. Klauda, M. Hodoscek, B. R. Brooks, and H. Lee Woodcock* CHARMMing: A New, Flexible, Web-based front-end to CHARMM. J. Chem. Inf. Mod.; 2008; 48(9); 1920-1929.
15. H. Lee Woodcock, B. R. Brooks, R. W. Pastor; Pathways and populations: Stereo-electronic insights into the exocyclic torsion of 5-hydroxy-methyl-tetrahydropyran. J. Am. Chem. Soc.; 2008; 130(20); 6345-6347.
14. N. H. Martin, R. M. Floyd, H. Lee Woodcock and S. Huffman; Computation of Through- Space NMR Shielding Effects in Aromatic Ring π-Stacked Complexes. J. Mol. Graphics Mod.; 2008; 26(7); 1125-1130.
13. H. Lee Woodcock, Milan Hodosceck, B. R. Brooks; Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms; J. Phys. Chem. A; 2007; 111(26); 5720-5728.
12. H. Lee Woodcock, R. W. Pastor, A. D. MacKerell, B. R. Brooks; Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate : 2-Ethoxy Tetrahydropyran. Biophys. J.; 2007; 93(1); 1-10.
11. H. Lee Woodcock, Damian Moran, Paul v.R. Schleyer, H.F. Schaefer; Carbene Stabilization by Aryl Substitudents. Is Bigger Better? J. Am. Chem. Soc.; 2007; 129(12); 3763-3770.
10. H. Lee Woodcock, Milan Hodosceck, Andrew T.B. Gilbert, Peter M.W. Gill, H.F. Schaefer, Bernard R. Brooks; Interfacing CHARMM and Q-Chem to perform QM/MM and QM/MM reaction pathway calculations. J. Comp. Chem.; 2007; 28(9); 1485-1502.
9. Y. Shao, L. Fusti-Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. T. Brown, A. T. B. Gilbert, L. V. lipchenko, S. V. Levchenko, D. P. ONeill, R. A. Distasio, R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley, J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele, V. A. Rassolov, P. E. Maslen, P. P. Korambath, R. D. Adamson, B. Austin, J. Baker, E. F. C. Byrd, H. Daschel, R. J. Doerksen, A. Dreuw, B. D. Dunietz, A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C. P. Hsu, G. Kedziora, R. Z. Khalliulin, P. Klunzinger, A. M. Lee, M. S. Lee, W. Liang, I. Lotan, N. Nair, B. Peters, E. I. Proynov, P. A. Pieniazek, Y. M. Rhee, J. Ritchie, E. Rosta, D. C. Sherrill, A. C. Simmonett, J. E. Subotnik, H. Lee Woodcock, W. Zhang, A. T. Bell, A. K. Chakraborty, D. M. Chipman, F. J. Keil, A. Warshel, W. J. Hehre, H. F. Schaefer, J. Kong, A. I. Krylov, P. M. W. Gill, M. Head-Gordon; Advances in methods and algorithms in a modern quantum chemistry program package. (Phys. Chem. Chem. Phys.); 2006; 8; 3172-3191.
8. Speakman LD, Papas BN, H. Lee Woodcock, Schaefer HF; A reinterpretation of microwave and infrared spectroscopic studies of benzaldehyde; J. Chem. Phys.; 2004; 120 (9); 4247-4250.
7. Papas BN, Wang SY, DeYonker NJ, H. Lee Woodcock, Schaefer HF; Naphthalenyl, anthracenyl, tetracenyl, and pentacenyl radicals and their anions; J. Phys. Chem. A; 2003; 107 (32); 6311-6316.
6. Moran D, H. Lee Woodcock, Chen ZF, Schaefer HF, Schleyer PvR; The viability of small endohedral hydrocarbon cage complexes: X@C4H4, X@C8H8, X@C8H14, X@C10H16, X@C12H12, and X@C16H16; J. Am. Chem. Soc.; 2003; 125 (37); 11442-11451.
5. H. Lee Woodcock, Milan Hodoscek, Paul Sherwood, Yong S. Lee, Henry F. Schaefer III, and Bernard R. Brooks; Exploring the QM/MM Replica Path Method: A Pathway Optimization of the Chorismate to Prephenate Claisen Rearrangement Catalyzed by Chorismate; Theor. Chem. Acc. 2003; 109(3); 140-148.
4. H. Lee Woodcock, H.F. Schaefer, P.R. Schreiner; Problematic energy differences between cumulenes and poly-ynes: Does this point to a systematic improvement of density functional theory? J. Phys. Chem. A 2002; 106(49) 11923-11931.
3. Ned H. Martin, Justin D. Brown, Kimberly H. Nance, Henry F. Schaefer III, Paul v. R. Schleyer, Zhi-Xiang Wang, and H. Lee Woodcock; Analysis of the Origin of Through-Space NMR (De)shielding by Selected Organic Functional Groups; Org. Lett.;2001; 3(24); 3823.
2. H. Lee Woodcock, Steven S. Wesolowski, Yukio Yamaguchi, and H.F. Schaefer; Systematic Study of the Neutral Radical PH2; J. Chem. Phys. 2001; 105(20); 5037.
1. H. Lee Woodcock, Damian Moran, Paul von Rague Schleyer and H.F. Schaefer; The Almost Bottleable Triplet Carbene: 2,6-dibromo-4-tert-butyl-2',6'-bistrifluoromethyl-4'-isopropyldiphenylcarbene; J. Am. Chem. Soc.; 2001; 123(18); 4331.