Search Results - "Woodcock, H"

Characterization and engineering of a plastic-degrading aromatic polyesterase by Austin, Harry P., Allen, Mark D., Donohoe, Bryon S., Rorrer, Nicholas A., Kearns, Fiona L., Silveira, Rodrigo L., Pollard, Benjamin C., Dominick, Graham, Duman, Ramona, Omari, Kamel El, Mykhaylyk, Vitaliy, Wagner, Armin, Michener, William E., Amore, Antonella, Skaf, Munir S., Crowley, Michael F., Thorne, Alan W., Johnson, Christopher W., Woodcock, H. Lee, McGeehan, John E., Beckham, Gregg T.

“…Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as…”
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Characterization and engineering of a two-enzyme system for plastics depolymerization by Knott, Brandon C., Erickson, Erika, Allen, Mark D., Gado, Japheth E., Graham, Rosie, Kearns, Fiona L., Pardo, Isabel, Topuzlu, Ece, Anderson, Jared J., Austin, Harry P., Dominick, Graham, Johnson, Christopher W., Rorrer, Nicholas A., Szostkiewicz, Caralyn J., Copié, Valérie, Payne, Christina M., Woodcock, H. Lee, Donohoe, Bryon S., Beckham, Gregg T., McGeehan, John E.

“…Plastics pollution represents a global environmental crisis. In response, microbes are evolving the capacity to utilize synthetic polymers as carbon and energy…”
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Convergence of single-step free energy perturbation by Boresch, Stefan, Woodcock, H. Lee

“…The convergence of free energy perturbation (Zwanzig's equation) and its non-equilibrium extension (Jarzynski's equation) is herein investigated from a…”
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The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations by Kearns, Fiona L, Warrensford, Luke, Boresch, Stefan, Woodcock, H Lee

“…Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when…”
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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 by Schöller, Andreas, Woodcock, H Lee, Boresch, Stefan

“…Non-equilibrium work switching simulations and Jarzynski's equation are a reliable method for computing free energy differences, ΔAlow→high, between two levels…”
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Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations by Schöller, Andreas, Kearns, Fiona, Woodcock, H. Lee, Boresch, Stefan

“…A key step during indirect alchemical free energy simulations using quantum mechanical/molecular mechanical (QM/MM) hybrid potential energy functions is the…”
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Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam by Pemberton, Orville A., Noor, Radwan E., M.V., Vasantha Kumar, Sanishvili, Ruslan, Kemp, M. Trent, Kearns, Fiona L., Woodcock, H. Lee, Gelis, Ioannis, Chen, Yu

“…Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The…”
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Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching by Hudson, Phillip S, Boresch, Stefan, Rogers, David M, Woodcock, H. Lee

“…The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles…”
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Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems by Hudson, Phillip S., Woodcock, H. Lee, Boresch, Stefan

“…Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area…”
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Use of Interaction Energies in QM/MM Free Energy Simulations by Hudson, Phillip S, Woodcock, H. Lee, Boresch, Stefan

“…The use of the most accurate (i.e., QM or QM/MM) levels of theory for free energy simulations (FES) is typically not possible. Primarily, this is because the…”
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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 by König, Gerhard, Hudson, Phillip S, Boresch, Stefan, Woodcock, H. Lee

“…The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method…”
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Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1‑Deoxy‑d‑xylulose-5-phosphate Synthase by Toci, Eucolona M., Austin, Steven L., Majumdar, Ananya, Woodcock, H. Lee, Freel Meyers, Caren L.

“…The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate…”
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EDTA functionalized silica for removal of Cu(II), Zn(II) and Ni(II) from aqueous solution by Kumar, R., Barakat, M.A., Daza, Y.A., Woodcock, H.L., Kuhn, J.N.

“…[Display omitted] •EDTA grafted silica was prepared and used as an adsorbent for Cu(II), Zn(II) and NI(II).•Adsorption of heavy metals followed pseudo-second…”
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Disaggregation is a Mechanism for Emission Turn-On of ortho-Aminomethylphenylboronic Acid-Based Saccharide Sensors by Chapin, Brette M, Metola, Pedro, Vankayala, Sai Lakshmana, Woodcock, H. Lee, Mooibroek, Tiddo J, Lynch, Vincent M, Larkin, Joseph D, Anslyn, Eric V

“…ortho-Aminomethylphenylboronic acid-based receptors with appended fluorophores are commonly used as molecular sensors for saccharides in aqueous media. The…”
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Reweighting from Molecular Mechanics Force Fields to the ANI-2x Neural Network Potential by Tkaczyk, Sara, Karwounopoulos, Johannes, Schöller, Andreas, Woodcock, H. Lee, Langer, Thierry, Boresch, Stefan, Wieder, Marcus

“…To achieve chemical accuracy in free energy calculations, it is necessary to accurately describe the system’s potential energy surface and efficiently sample…”
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Not Drug-like, but Like Drugs: Cnidaria Natural Products by Laguionie-Marchais, Claire, Allcock, A Louise, Baker, Bill J, Conneely, Ellie-Ann, Dietrick, Sarah G, Kearns, Fiona, McKeever, Kate, Young, Ryan M, Sierra, Connor A, Soldatou, Sylvia, Woodcock, H Lee, Johnson, Mark P

“…Phylum Cnidaria has been an excellent source of natural products, with thousands of metabolites identified. Many of these have not been screened in bioassays…”
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Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale by Hudson, Phillip S., Han, Kyungreem, Woodcock, H. Lee, Brooks, Bernard R.

“…Use of quantum mechanical/molecular mechanical (QM/MM) methods in binding free energy calculations, particularly in the SAMPL challenge, often fail to achieve…”
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Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations by Woodcock III, H. Lee, Hodošček, Milan, Gilbert, Andrew T. B., Gill, Peter M. W., Schaefer III, Henry F., Brooks, Bernard R.

“…A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree‐Fock, density functional theory (DFT), and post‐HF (RIMP2, MP2,…”
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CIFDock: A novel CHARMM‐based flexible receptor–flexible ligand docking protocol by Vankayala, Sai L., Warrensford, Luke C., Pittman, Amanda R., Pollard, Benjamin C., Kearns, Fiona L., Larkin, Joseph D., Woodcock, H. Lee

“…Docking studies play a critical role in the current workflow of drug discovery. However, limitations may often arise through factors including inadequate…”
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Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X‑ray Crystallography by Nichols, Derek A, Hargis, Jacqueline C, Sanishvili, Ruslan, Jaishankar, Priyadarshini, Defrees, Kyle, Smith, Emmanuel W, Wang, Kenneth K, Prati, Fabio, Renslo, Adam R, Woodcock, H. Lee, Chen, Yu

“…Ligand binding can change the pK a of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of…”
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