Search Results - "Horton, Joshua T."

An open-source molecular builder and free energy preparation workflow by Bieniek, Mateusz K., Cree, Ben, Pirie, Rachael, Horton, Joshua T., Tatum, Natalie J., Cole, Daniel J.

“…Automated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity,…”
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QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics by Horton, Joshua T, Allen, Alice E. A, Dodda, Leela S, Cole, Daniel J

“…Modern molecular mechanics force fields are widely used for modeling the dynamics and interactions of small organic molecules using libraries of transferable…”
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Exploration and validation of force field design protocols through QM-to-MM mapping by Ringrose, Chris, Horton, Joshua T, Wang, Lee-Ping, Cole, Daniel J

“…The scale of the parameter optimisation problem in traditional molecular mechanics force field construction means that design of a new force field is a long…”
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Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field by Boothroyd, Simon, Behara, Pavan Kumar, Madin, Owen C., Hahn, David F., Jang, Hyesu, Gapsys, Vytautas, Wagner, Jeffrey R., Horton, Joshua T., Dotson, David L., Thompson, Matthew W., Maat, Jessica, Gokey, Trevor, Wang, Lee-Ping, Cole, Daniel J., Gilson, Michael K., Chodera, John D., Bayly, Christopher I., Shirts, Michael R., Mobley, David L.

“…We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration,…”
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“O's for Oblivion:” Ephemeral Bibelots and Trans Subcultural Production1 by Horton, Joshua T

“…What differentiates Le Petit Journal des Refusees from the magazine culture of the 19th century is that it is an early example of the short-lived little…”
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Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale by Horton, Joshua T., Boothroyd, Simon, Wagner, Jeffrey, Mitchell, Joshua A., Gokey, Trevor, Dotson, David L., Behara, Pavan Kumar, Ramaswamy, Venkata Krishnan, Mackey, Mark, Chodera, John D., Anwar, Jamshed, Mobley, David L., Cole, Daniel J.

“…The development of accurate transferable force fields is key to realizing the full potential of atomistic modeling in the study of biological processes such as…”
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Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field by Yang, Lupeng, Horton, Joshua T, Payne, Michael C, Penfold, Thomas J, Cole, Daniel J

“…Combined molecular dynamics (MD) and quantum mechanics (QM) simulation procedures have gained popularity in modeling the spectral properties of functional…”
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The future of force fields in computer-aided drug design by Cole, Daniel J, Horton, Joshua T, Nelson, Lauren, Kurdekar, Vadiraj

“…In structure-based computer-aided drug design (CADD), virtual screening aims to suggest new drug candidates by docking large libraries of small molecules into…”
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Fast, conformation-independent charges with graph convolutional networks by Wang, Lily, Boothroyd, Simon, Horton, Joshua T., Thompson, Matthew W., Shirts, Michael R., Cole, Daniel J., Chodera, John D., Mobley, David L.

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Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields by Behara, Pavan Kumar, Jang, Hyesu, Horton, Joshua T., Gokey, Trevor, Dotson, David L., Boothroyd, Simon, Bayly, Christopher I., Cole, Daniel J., Wang, Lee-Ping, Mobley, David L.

“…A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical…”
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Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field by D’Amore, Lorenzo, Hahn, David F., Dotson, David L., Horton, Joshua T., Anwar, Jamshed, Craig, Ian, Fox, Thomas, Gobbi, Alberto, Lakkaraju, Sirish Kaushik, Lucas, Xavier, Meier, Katharina, Mobley, David L., Narayanan, Arjun, Schindler, Christina E. M., Swope, William C., in ’t Veld, Pieter J., Wagner, Jeffrey, Xue, Bai, Tresadern, Gary

“…Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein–ligand binding…”
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Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations by Nelson, Lauren, Bariami, Sofia, Ringrose, Chris, Horton, Joshua T, Kurdekar, Vadiraj, Mey, Antonia S. J. S, Michel, Julien, Cole, Daniel J

“…The quantum mechanical bespoke (QUBE) force-field approach has been developed to facilitate the automated derivation of potential energy function parameters…”
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Development and benchmarking of an open, self-consistent force field for proteins and small molecules from the open force field initiative by Cavender, Chapin E., Behara, Pavan K., Boothroyd, Simon, Dotson, David L., Horton, Joshua T., Mitchell, Joshua A., Pulido, Ivan, Thompson, Matthew W., Wagner, Jeffrey, Wang, Lily, Chodera, John D., Cole, Daniel J., Mobley, David L., Shirts, Michael R., Gilson, Michael K.

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A transferable double exponential potential for condensed phase simulations of small molecules by Horton, Joshua T, Boothroyd, Simon, Behara, Pavan Kumar, Mobley, David L, Cole, Daniel J

“…The Lennard-Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed…”
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Panic on the Streets of London: Masculine Identity and Homosexual Panic in Neil Gaiman's "How to Talk to Girls at Parties" by Horton, Joshua T

“…Now, more and more people are coming out of the "closet," a metonymical representation of both oppression and repression. Understanding the complicated process…”
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“O's for Oblivion:” Ephemeral Bibelots and Trans Subcultural Production 1 by Horton, Joshua T

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An open-source molecular builder and free energy preparation workflow by Bieniek, Mateusz K, Cree, Ben, Pirie, Rachael, Horton, Joshua T, Tatum, Natalie J, Cole, Daniel J

“…Automated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity,…”
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MACE-OFF23: Transferable Machine Learning Force Fields for Organic Molecules by Kovács, Dávid Péter, Moore, J. Harry, Browning, Nicholas J, Batatia, Ilyes, Horton, Joshua T, Kapil, Venkat, Witt, William C, Magdău, Ioan-Bogdan, Cole, Daniel J, Csányi, Gábor

“…Classical empirical force fields have dominated biomolecular simulation for over 50 years. Although widely used in drug discovery, crystal structure…”
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