المؤلفون: Setiadi, Jeffry, Boothroyd, Simon, Slochower, David R, Dotson, David L, Thompson, Matthew W, Wagner, Jeffrey R, Wang, Lee-Ping, Gilson, Michael K

المصدر: Journal of Chemical Theory and Computation. 20(1)

مصطلحات موضوعية: Medicinal and Biomolecular Chemistry, Chemical Sciences, Generic health relevance, Ligands, Proteins, Software, Protein Binding, Solvents, Thermodynamics, Molecular Dynamics Simulation, Theoretical and Computational Chemistry, Biochemistry and Cell Biology, Computer Software, Chemical Physics, Physical chemistry, Theoretical and computational chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/2ts1v38g
https://escholarship.org/content/qt2ts1v38g/qt2ts1v38g.pdf

المؤلفون: 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

المصدر: Journal of Chemical Theory and Computation. 19(11)

مصطلحات موضوعية: Medicinal and Biomolecular Chemistry, Chemical Sciences, Theoretical and Computational Chemistry, Networking and Information Technology R&D (NITRD), Benchmarking, Ligands, Proteins, Thermodynamics, Entropy, Biochemistry and Cell Biology, Computer Software, Chemical Physics, Physical chemistry, Theoretical and computational chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/35b7v1pz
https://escholarship.org/content/qt35b7v1pz/qt35b7v1pz.pdf

المؤلفون: 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.

مصطلحات موضوعية: Physics - Chemical Physics, Computer Science - Machine Learning, Quantitative Biology - Biomolecules

URL الوصول: http://arxiv.org/abs/2209.10702

المؤلفون: 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 EM, Swope, William C, Veld, Pieter J in ’t, Wagner, Jeffrey, Xue, Bai, Tresadern, Gary

المصدر: Journal of Chemical Information and Modeling. 62(23)

مصطلحات موضوعية: Medicinal and Biomolecular Chemistry, Chemical Sciences, Generic health relevance, Thermodynamics, Ligands, Proteins, Physical Phenomena, Theoretical and Computational Chemistry, Computation Theory and Mathematics, Medicinal & Biomolecular Chemistry, Medicinal and biomolecular chemistry, Theoretical and computational chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/1b0484cn

المؤلفون: 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

المصدر: Journal of Chemical Information and Modeling. 62(22)

مصطلحات موضوعية: Medicinal and Biomolecular Chemistry, Chemical Sciences, Theoretical and Computational Chemistry, Ligands, Proteins, Software, Entropy, Protein Binding, Computation Theory and Mathematics, Medicinal & Biomolecular Chemistry, Medicinal and biomolecular chemistry, Theoretical and computational chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/1s0235vp
https://escholarship.org/content/qt1s0235vp/qt1s0235vp.pdf

المؤلفون: Smith, Daniel GA, Lolinco, Annabelle T, Glick, Zachary L, Lee, Jiyoung, Alenaizan, Asem, Barnes, Taylor A, Borca, Carlos H, Di Remigio, Roberto, Dotson, David L, Ehlert, Sebastian, Heide, Alexander G, Herbst, Michael F, Hermann, Jan, Hicks, Colton B, Horton, Joshua T, Hurtado, Adrian G, Kraus, Peter, Kruse, Holger, Lee, Sebastian JR, Misiewicz, Jonathon P, Naden, Levi N, Ramezanghorbani, Farhad, Scheurer, Maximilian, Schriber, Jeffrey B, Simmonett, Andrew C, Steinmetzer, Johannes, Wagner, Jeffrey R, Ward, Logan, Welborn, Matthew, Altarawy, Doaa, Anwar, Jamshed, Chodera, John D, Dreuw, Andreas, Kulik, Heather J, Liu, Fang, Martínez, Todd J, Matthews, Devin A, Schaefer, Henry F, Šponer, Jiří, Turney, Justin M, Wang, Lee-Ping, De Silva, Nuwan, King, Rollin A, Stanton, John F, Gordon, Mark S, Windus, Theresa L, Sherrill, C David, Burns, Lori A

المصدر: The Journal of Chemical Physics. 155(20)

مصطلحات موضوعية: Networking and Information Technology R&D (NITRD), Physical Sciences, Chemical Sciences, Engineering, Chemical Physics

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/4h8041v9

المؤلفون: 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.

المساهمون: UK Research and Innovation, American Chemical Society Petroleum Research Fund, National Institute of General Medical Sciences

المصدر: The Journal of Physical Chemistry B ; volume 128, issue 32, page 7888-7902 ; ISSN 1520-6106 1520-5207

الاتاحة: https://doi.org/10.1021/acs.jpcb.4c03167
https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.4c03167

المؤلفون: Cavender, Chapin E., Behara, Pavan K., Boothroyd, Simon, Dotson, David L., Horton, Joshua T., Mitchell, Joshua A., Pulido, Ivan J., Thompson, Matthew W., Wagner, Jeffrey, Wang, Lily, Chodera, John D., Cole, Daniel J., Mobley, David L., Shirts, Michael R., Gilson, Michael K.

مصطلحات موضوعية: Force Field, Protein, NMR

Relation: https://zenodo.org/communities/openforcefield; https://doi.org/10.5281/zenodo.7696578; https://doi.org/10.5281/zenodo.7696579; oai:zenodo.org:7696579

الاتاحة: https://doi.org/10.5281/zenodo.7696579

المؤلفون: 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.

مصطلحات موضوعية: Protein-ligand binding, accuracy, database

وصف الملف: application/pdf

Relation: 11; http://hdl.handle.net/10919/114246; https://doi.org/10.1038/s41597-022-01882-6; 10

الاتاحة: http://hdl.handle.net/10919/114246
https://doi.org/10.1038/s41597-022-01882-6

المؤلفون: Cavender, Chapin E, Behara, Pavan K, Boothroyd, Simon, Dotson, David L, Gapsys, Vyautas, Hahn, David F, Horton, Josha T, Pulido, Ivan J, Thompson, Matthew W, Wager, Jeffrey, Wang, Lily, Chodera, John D, Cole, Daniel J, Mobley, David L, Shirts, Michael R, Gilson, Michael K

المصدر: BPS 2022, 66th Annual Meeting of the Biophysical Society, San Fransisco, CA, USA, 2022-02-19 to 2022-02-23

مصطلحات موضوعية: Biopolymer force field, Open source software

Relation: https://zenodo.org/communities/openforcefield; https://doi.org/10.5281/zenodo.6153445; https://doi.org/10.5281/zenodo.6153446; oai:zenodo.org:6153446

الاتاحة: https://doi.org/10.5281/zenodo.6153446

المؤلفون: 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.

المصدر: Biophysical Journal ; volume 121, issue 3, page 272a ; ISSN 0006-3495

الاتاحة: http://dx.doi.org/10.1016/j.bpj.2021.11.1367
https://api.elsevier.com/content/article/PII:S0006349521023420?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0006349521023420?httpAccept=text/plain

المؤلفون: Cavender, Chapin E., Behara, Pavan K., Dotson, David L., Friedman, Anika J., Gokey, Trevor, Horton, Joshua T., Pulido, Ivan, Thompson, Matthew W., Wagner, Jeffrey, Wang, Lily, Chodera, John D., Cole, Daniel J., Mobley, David L., Shirts, Michael R., Gilson, Michael K.

المصدر: Biophysical Journal ; volume 123, issue 3, page 421a ; ISSN 0006-3495

الاتاحة: http://dx.doi.org/10.1016/j.bpj.2023.11.2562
https://api.elsevier.com/content/article/PII:S0006349523032630?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0006349523032630?httpAccept=text/plain

المؤلفون: Dotson, David L., Kenney, Ian M., Beckstein, Oliver, Liu, Shuai, Jensen, Travis, Allen, Bryce, Wille, Dominik, Lim, Victoria, Lee, Hyungro, Barhaghi, Mohammad Soroush, Wu, Zhiyi, Hsu, Wei-Tse, Schlaich, Alexander, Hénin, Jérôme, Joseph, Thomas T., Alibay, Irfan, Merz, Pascal T., Marson, Domenico, Fan, Shujie, Janssen, Jan, Li, Haoxi, Carter, Helmut, Mobley, David, Shirts, Michael R., Clark, Jennifer A.

مصطلحات موضوعية: Python, free energy, molecular dynamics, alchemistry

Relation: https://github.com/alchemistry/alchemlyb/tree/2.4.1; https://doi.org/10.5281/zenodo.596103; https://doi.org/10.5281/zenodo.13799342; oai:zenodo.org:13799342

الاتاحة: https://doi.org/10.5281/zenodo.13799342

المؤلفون: Dotson, David L., Kenney, Ian M., Beckstein, Oliver, Liu, Shuai, Jensen, Travis, Allen, Bryce, Wille, Dominik, Lim, Victoria, Lee, Hyungro, Barhaghi, Mohammad Soroush, Wu, Zhiyi, Hsu, Wei-Tse, Schlaich, Alexander, Hénin, Jérôme, Joseph, Thomas T., Alibay, Irfan, Merz, Pascal T., Marson, Domenico, Fan, Shujie, Janssen, Jan, Li, Haoxi, Carter, Helmut, Mobley, David, Shirts, Michael R., Clark, Jennifer A.

مصطلحات موضوعية: Python, free energy, molecular dynamics, alchemistry

Relation: https://github.com/alchemistry/alchemlyb/tree/2.4.0; https://doi.org/10.5281/zenodo.596103; https://doi.org/10.5281/zenodo.13774657; oai:zenodo.org:13774657

الاتاحة: https://doi.org/10.5281/zenodo.13774657

المؤلفون: Beckstein, Oliver, Kenney, Ian M., Zhang, Chenou, Naughton, Fiona, Sexton, Rick, Fan, Shujie, Dotson, David L.

المصدر: Biophysical Journal ; volume 118, issue 3, page 19a ; ISSN 0006-3495

الاتاحة: http://dx.doi.org/10.1016/j.bpj.2019.11.288
https://api.elsevier.com/content/article/PII:S0006349519312172?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0006349519312172?httpAccept=text/plain

المؤلفون: 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.

المصدر: The Journal of General Physiology. 144(6):529-544

مصطلحات موضوعية: Biochemistry, biokemi

وصف الملف: print

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-111902
https://doi.org/10.1085/jgp.201411219

المؤلفون: 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.

مصطلحات الفهرس: Protein-ligand binding, accuracy, database, Article - Refereed

URL: http://hdl.handle.net/10919/114246

المؤلفون: Cavender, Chapin E., Behara, Pavan K., Boothroyd, Simon, Dotson, David L., Gokey, Trevor, Horton, Joshua T., Mitchell, Joshua A., Pulido, Ivan J., Thompson, Matthew W., Wagner, Jeffrey, Wang, Lily, Chodera, John D., Cole, Daniel J., Mobley, David L., Shirts, Michael R., Gilson, Michael K.

مصطلحات موضوعية: Force Field, Protein, NMR

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0608e40d44c7b3161d56f2ad943268a7

المؤلفون: 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, Levy, Haim, Lithgo, Ryan M, Logvinenko, Ivan G, Lukacik, Petra, Macdonald, Hannah Bruce, MacLean, Elizabeth M, Makower, Laetitia L, Malla, Tika R, Marples, Peter G, Matviiuk, Tatiana, McCorkindale, Willam, McGovern, Briana L, Melamed, Sharon, Melnykov, Kostiantyn P, Michurin, Oleg, Miesen, Pascal, Mikolajek, Halina, Milne, Bruce F, Minh, David, Morris, Aaron, Morris, Garrett M, Morwitzer, Melody Jane, Moustakas, Demetri, Mowbray, Charles E, Nakamura, Aline M, Neto, Jose Brandao, Neyts, Johan, Nguyen, Luong, Noske, Gabriela D, Oleinikovas, Vladas, Oliva, Glaucius, Overheul, Gijs J, Owen, C David, Pai, Ruby, Pan, Jin, Paran, Nir, Payne, Alexander Matthew, Perry, Benjamin, Pingle, Maneesh, Pinjari, Jakir, Politi, Boaz, Powell, Ailsa, Pšenák, Vladimír, Pulido, Iván, Puni, Reut, Rangel, Victor L, Reddi, Rambabu N, Rees, Paul, Reid, St Patrick, Reid, Lauren, Resnick, Efrat, Ripka, Emily Grace, Robinson, Ralph P, Rodriguez-Guerra, Jaime, Rosales, Romel, Rufa, Dominic A, Saar, Kadi, Saikatendu, Kumar Singh, Salah, Eidarus, Schaller, David, Scheen, Jenke, Schiffer, Celia A, Schofield, Christopher J, Shafeev, Mikhail, Shaikh, Aarif, Shaqra, Ala M, Shi, Jiye, Shurrush, Khriesto, Singh, Sukrit, Sittner, Assa, Sjö, Peter, Skyner, Rachael, Smalley, Adam, Smeets, Bart, Smilova, Mihaela D, Solmesky, Leonardo J, Spencer, John, Strain-Damerell, Claire, Swamy, Vishwanath, Tamir, Hadas, Taylor, Jenny C, Tennant, Rachael E, Thompson, Warren, Thompson, Andrew, Tomásio, Susana, Tomlinson, Charles W E, Tsurupa, Igor S, Tumber, Anthony, Vakonakis, Ioannis, van Rij, Ronald P, Vangeel, Laura, Varghese, Finny S, Vaschetto, Mariana, Vitner, Einat B, Voelz, Vincent, Volkamer, Andrea, Walsh, Martin A, Ward, Walter, Weatherall, Charlie, Weiss, Shay, White, Kris M, Wild, Conor Francis, Witt, Karolina D, Wittmann, Matthew, Wright, Nathan, Yahalom-Ronen, Yfat, Yilmaz, Nese Kurt, Zaidmann, Daniel, Zhang, Ivy, Zidane, Hadeer, Zitzmann, Nicole, Zvornicanin, Sarah N

المساهمون: Biochemistry and Molecular Biotechnology, Morningside Graduate School of Biomedical Sciences, Schiffer Lab, Qiu Yu Judy Huang

المصدر: Science (New York, N.Y.) ; 382 ; 6671 ; eabo7201 ; United States

Relation: Science; https://doi.org/10.1126/science.abo7201; Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC; COVID Moonshot Consortium‡; Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, Aschenbrenner JC, Balcomb BH, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Bilenko VA, Borden B, Boulet P, Bowman GR, Brewitz L, Brun J, Bvnbs S, Calmiano M, Carbery A, Carney DW, Cattermole E, Chang E, Chernyshenko E, Clyde A, Coffland JE, Cohen G, Cole JC, Contini A, Cox L, Croll TI, Cvitkovic M, De Jonghe S, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett LE, Eastman P, Erez N, Eyermann CJ, Fairhead M, Fate G, Fedorov O, Fernandes RS, Ferrins L, Foster R, Foster H, Fraisse L, Gabizon R, García-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen RC, Glinert I, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Haneef A, Hassell Hart S, Heer J, Henry M, Hill M, Horrell S, Huang QYJ, Huliak VD, Hurley MFD, Israely T, Jajack A, Jansen J, Jnoff E, Jochmans D, John T, Kaminow B, Kang L, Kantsadi AL, Kenny PW, Kiappes JL, Kinakh SO, Kovar B, Krojer T, La VNT, Laghnimi-Hahn S, Lefker BA, Levy H, Lithgo RM, Logvinenko IG, Lukacik P, Macdonald HB, MacLean EM, Makower LL, Malla TR, Marples PG, Matviiuk T, McCorkindale W, McGovern BL, Melamed S, Melnykov KP, Michurin O, Miesen P, Mikolajek H, Milne BF, Minh D, Morris A, Morris GM, Morwitzer MJ, Moustakas D, Mowbray CE, Nakamura AM, Neto JB, Neyts J, Nguyen L, Noske GD, Oleinikovas V, Oliva G, Overheul GJ, Owen CD, Pai R, Pan J, Paran N, Payne AM, Perry B, Pingle M, Pinjari J, Politi B, Powell A, Pšenák V, Pulido I, Puni R, Rangel VL, Reddi RN, Rees P, Reid SP, Reid L, Resnick E, Ripka EG, Robinson RP, Rodriguez-Guerra J, Rosales R, Rufa DA, Saar K, Saikatendu KS, Salah E, Schaller D, Scheen J, Schiffer CA, Schofield CJ, Shafeev M, Shaikh A, Shaqra AM, Shi J, Shurrush K, Singh S, Sittner A, Sjö P, Skyner R, Smalley A, Smeets B, Smilova MD, Solmesky LJ, Spencer J, Strain-Damerell C, Swamy V, Tamir H, Taylor JC, Tennant RE, Thompson W, Thompson A, Tomásio S, Tomlinson CWE, Tsurupa IS, Tumber A, Vakonakis I, van Rij RP, Vangeel L, Varghese FS, Vaschetto M, Vitner EB, Voelz V, Volkamer A, Walsh MA, Ward W, Weatherall C, Weiss S, White KM, Wild CF, Witt KD, Wittmann M, Wright N, Yahalom-Ronen Y, Yilmaz NK, Zaidmann D, Zhang I, Zidane H, Zitzmann N, Zvornicanin SN. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science. 2023 Nov 10;382(6671):eabo7201. doi:10.1126/science.abo7201. Epub 2023 Nov 10. PMID: 37943932.; http://hdl.handle.net/20.500.14038/52849; Science (New York, N.Y.)

الاتاحة: https://doi.org/10.1126/science.abo7201
https://hdl.handle.net/20.500.14038/52849

المؤلفون: Swenson, David W.H., Alibay, Irfan, Dotson, David L., Ries, Benjamin, Henry, Mike M., Baumann, Hannah, Eastwood, James Baggs, Mitchell, Josh, Gowers, Richard J.

المصدر: US-RSE'23, Annual Conference of the United States Research Software Engineer Association, Chicago, IL, 16-18 October 2023

Relation: https://zenodo.org/communities/openfreeenergy; https://doi.org/10.5281/zenodo.10023085; https://doi.org/10.5281/zenodo.10023086; oai:zenodo.org:10023086

الاتاحة: https://doi.org/10.5281/zenodo.10023086