Search Results - "Dotson, David L."

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA by Huang, Yandong, Chen, Wei, Dotson, David L., Beckstein, Oliver, Shen, Jana

“…Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical…”
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A two-domain elevator mechanism for sodium/proton antiport by Lee, Chiara, Kang, Hae Joo, von Ballmoos, Christoph, Newstead, Simon, Uzdavinys, Povilas, Dotson, David L., Iwata, So, Beckstein, Oliver, Cameron, Alexander D., Drew, David

“…The X-ray crystal structure of NapA, a Na + /H + antiporter from Thermus thermophilus , in an active, outward-facing state is reported; comparisons to the…”
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SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials by Eastman, Peter, Behara, Pavan Kumar, Dotson, David L., Galvelis, Raimondas, Herr, John E., Horton, Josh T., Mao, Yuezhi, Chodera, John D., Pritchard, Benjamin P., Wang, Yuanqing, De Fabritiis, Gianni, Markland, Thomas E.

“…Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train…”
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Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights by Lee, Chiara, Yashiro, Shoko, Dotson, David L, Uzdavinys, Povilas, Iwata, So, Sansom, Mark S P, von Ballmoos, Christoph, Beckstein, Oliver, Drew, David, Cameron, Alexander D

“…Sodium-proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How…”
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Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters by Coincon, Mathieu, Uzdavinys, Povilas, Nji, Emmanuel, Dotson, David L, Winkelmann, Iven, Abdul-Hussein, Saba, Cameron, Alexander D, Beckstein, Oliver, Drew, David

“…New crystal structures of the NapA antiporter in both outward- and inward-facing conformations provide evidence for an elevator-like ion-translocation…”
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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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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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Tuning Potential Functions to Host–Guest Binding Data by Setiadi, Jeffry, Boothroyd, Simon, Slochower, David R., Dotson, David L., Thompson, Matthew W., Wagner, Jeffrey R., Wang, Lee-Ping, Gilson, Michael K.

“…Software to more rapidly and accurately predict protein–ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods…”
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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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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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Climate action and growing electricity demand: Meeting both challenges in the 21st century with space-based solar power delivered by space elevator by Dotson, David L., Eddy, Jerry, Swan, Peter

“…Global climate action is the grand challenge of the 21st century. Large reductions in greenhouse gas emissions are needed, with net-zero CO2 emissions by…”
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Molecular Mechanism of Alternating-access Transport in a Sodium/Proton Antiporter by Beckstein, Oliver, Kenney, Ian M., Zhang, Chenou, Naughton, Fiona, Sexton, Rick, Fan, Shujie, Dotson, David L.

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Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors by Boby, Melissa L, Fearon, Daren, Ferla, Matteo, Filep, Mihajlo, Koekemoer, Lizbé, Robinson, Matthew C, Chodera, John D, Lee, Alpha A, London, Nir, von Delft, Annette, von Delft, Frank, Achdout, Hagit, Aimon, Anthony, Alonzi, Dominic S, Arbon, Robert, Aschenbrenner, Jasmin C, Balcomb, Blake H, Bar-David, Elad, Barr, Haim, Ben-Shmuel, Amir, Bennett, James, Bilenko, Vitaliy A, Borden, Bruce, Boulet, Pascale, Bowman, Gregory R, Brewitz, Lennart, Brun, Juliane, Bvnbs, Sarma, Calmiano, Mark, Carbery, Anna, Carney, Daniel W, Cattermole, Emma, Chang, Edcon, Chernyshenko, Eugene, Clyde, Austin, Coffland, Joseph E, Cohen, Galit, Cole, Jason C, Contini, Alessandro, Cox, Lisa, Croll, Tristan Ian, Cvitkovic, Milan, De Jonghe, Steven, Dias, Alex, Donckers, Kim, Dotson, David L, Douangamath, Alice, Duberstein, Shirly, Dudgeon, Tim, Dunnett, Louise E, Eastman, Peter, Erez, Noam, Eyermann, Charles J, Fairhead, Michael, Fate, Gwen, Fedorov, Oleg, Fernandes, Rafaela S, Ferrins, Lori, Foster, Richard, Foster, Holly, Fraisse, Laurent, Gabizon, Ronen, García-Sastre, Adolfo, Gawriljuk, Victor O, Gehrtz, Paul, Gileadi, Carina, Giroud, Charline, Glass, William G, Glen, Robert C, Glinert, Itai, Godoy, Andre S, Gorichko, Marian, Gorrie-Stone, Tyler, Griffen, Ed J, Haneef, Amna, Hassell Hart, Storm, Heer, Jag, Henry, Michael, Hill, Michelle, Horrell, Sam, Huang, Qiu Yu Judy, Huliak, Victor D, Hurley, Matthew F D, Israely, Tomer, Jajack, Andrew, Jansen, Jitske, Jnoff, Eric, Jochmans, Dirk, John, Tobias, Kaminow, Benjamin, Kang, Lulu, Kantsadi, Anastassia L, Kenny, Peter W, Kiappes, J L, Kinakh, Serhii O, Kovar, Boris, Krojer, Tobias, La, Van Ngoc Thuy, Laghnimi-Hahn, Sophie, Lefker, Bruce A

“…We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute…”
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Building an open, self-consistent force field for biopolymers and small molecules with the open force field initiative infrastructure by Cavender, Chapin E., Behara, Pavan K., Boothroyd, Simon, Dotson, David L., Pulido, Ivan J., Thompson, Matthew W., Wagner, Jeffrey, Wang, Lily, Chodera, John D., Mobley, David L., Shirts, Michael R., Gilson, Michael K.

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Molecular Mechanism of Electrogenic Sodium/Proton Antiport by Beckstein, Oliver, Dotson, David L., Coincon, Mathieu, Huang, Yandong, Lee, Chiara, Uzdavinys, Povilas, Nji, Emmanuel, Yashiro, Shoko, Chen, Wei, Cameron, Alexander D., Shen, Jana, Drew, David

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alchemlyb: the simple alchemistry library by Wu, Zhiyi, Dotson, David L., Alibay, Irfan, Allen, Bryce K., Barhaghi, Mohammad Soroush, Hénin, Jérôme, Joseph, Thomas T., Kenney, Ian M., Lee, Hyungro, Li, Haoxi, Lim, Victoria, Liu, Shuai, Marson, Domenico, Merz, Pascal T., Schlaich, Alexander, Mobley, David, Shirts, Michael R., Beckstein, Oliver

“…alchemlyb is an open-source Python software package for the analysis of alchemical free energycalculations, an important method in computational chemistry and…”
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Mechanism of Sodium/Proton Antiport in NhaA by Beckstein, Oliver, Dotson, David L., Lee, Chiara N., Drew, David, Cameron, Alexander D.

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Investigating the Conformational Dynamics of DNA with Lesions through Fluorescence-Based Technniques and Computer Simulations by Stennett, Elana M.S., Dotson, David L., Denning, Elizabeth J., Beckstein, Oliver, Levitus, Marcia

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Recent Structures and Molecular Dynamics Simulations Offer New Perspective on Na+/H+ Antiporters by Dotson, David L., Lee, Chiara, Yashiro, Shoko, Uzdavinys, Povilas, von Ballmoos, Christoph, Drew, David, Cameron, Alexander D., Beckstein, Oliver

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