OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, Peter, Swails, Jason, Chodera, John D, McGibbon, Robert T, Zhao, Yutong, Beauchamp, Kyle A, Wang, Lee-Ping, Simmonett, Andrew C, Harrigan, Matthew P, Stern, Chaya D, Wiewiora, Rafal P, Brooks, Bernard R, Pande, Vijay S
Published in PLoS computational biology (01.07.2017)
Published in PLoS computational biology (01.07.2017)
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Markov models of molecular kinetics: generation and validation
Prinz, Jan-Hendrik, Wu, Hao, Sarich, Marco, Keller, Bettina, Senne, Martin, Held, Martin, Chodera, John D, Schütte, Christof, Noé, Frank
Published in The Journal of chemical physics (07.05.2011)
Published in The Journal of chemical physics (07.05.2011)
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SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome
Zimmerman, Maxwell I., Porter, Justin R., Ward, Michael D., Singh, Sukrit, Vithani, Neha, Meller, Artur, Mallimadugula, Upasana L., Kuhn, Catherine E., Borowsky, Jonathan H., Wiewiora, Rafal P., Hurley, Matthew F. D., Harbison, Aoife M., Fogarty, Carl A., Coffland, Joseph E., Fadda, Elisa, Voelz, Vincent A., Chodera, John D., Bowman, Gregory R.
Published in Nature chemistry (01.07.2021)
Published in Nature chemistry (01.07.2021)
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L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH
Intlekofer, Andrew M, Wang, Bo, Liu, Hui, Shah, Hardik, Carmona-Fontaine, Carlos, Rustenburg, Ariën S, Salah, Salah, Gunner, M R, Chodera, John D, Cross, Justin R, Thompson, Craig B
Published in Nature chemical biology (01.05.2017)
Published in Nature chemical biology (01.05.2017)
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Hypoxia Induces Production of L-2-Hydroxyglutarate
Intlekofer, Andrew M., Dematteo, Raymond G., Venneti, Sriram, Finley, Lydia W.S., Lu, Chao, Judkins, Alexander R., Rustenburg, Ariën S., Grinaway, Patrick B., Chodera, John D., Cross, Justin R., Thompson, Craig B.
Published in Cell metabolism (04.08.2015)
Published in Cell metabolism (04.08.2015)
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The Ribosome Modulates Nascent Protein Folding
Kaiser, Christian M., Goldman, Daniel H., Chodera, John D., Tinoco, Ignacio, Bustamante, Carlos
Published in Science (American Association for the Advancement of Science) (23.12.2011)
Published in Science (American Association for the Advancement of Science) (23.12.2011)
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Alchemical free energy methods for drug discovery: progress and challenges
Chodera, John D, Mobley, David L, Shirts, Michael R, Dixon, Richard W, Branson, Kim, Pande, Vijay S
Published in Current opinion in structural biology (01.04.2011)
Published in Current opinion in structural biology (01.04.2011)
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Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations
Intlekofer, Andrew M., Shih, Alan H., Wang, Bo, Nazir, Abbas, Rustenburg, Ariën S., Albanese, Steven K., Patel, Minal, Famulare, Christopher, Correa, Fabian M., Takemoto, Naofumi, Durani, Vidushi, Liu, Hui, Taylor, Justin, Farnoud, Noushin, Papaemmanuil, Elli, Cross, Justin R., Tallman, Martin S., Arcila, Maria E., Roshal, Mikhail, Petsko, Gregory A., Wu, Bin, Choe, Sung, Konteatis, Zenon D., Biller, Scott A., Chodera, John D., Thompson, Craig B., Levine, Ross L., Stein, Eytan M.
Published in Nature (London) (01.07.2018)
Published in Nature (London) (01.07.2018)
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Current Status of the AMOEBA Polarizable Force Field
Ponder, Jay W, Wu, Chuanjie, Ren, Pengyu, Pande, Vijay S, Chodera, John D, Schnieders, Michael J, Haque, Imran, Mobley, David L, Lambrecht, Daniel S, DiStasio, Robert A, Head-Gordon, Martin, Clark, Gary N. I, Johnson, Margaret E, Head-Gordon, Teresa
Published in The journal of physical chemistry. B (04.03.2010)
Published in The journal of physical chemistry. B (04.03.2010)
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Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model
Morris, Aaron, McCorkindale, William, Drayman, Nir, Chodera, John D., Tay, Savas, London, Nir, Lee, Alpha A.
Published in Chemical communications (Cambridge, England) (18.06.2021)
Published in Chemical communications (Cambridge, England) (18.06.2021)
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MEN1 mutations mediate clinical resistance to menin inhibition
Perner, Florian, Stein, Eytan M., Wenge, Daniela V., Singh, Sukrit, Kim, Jeonghyeon, Apazidis, Athina, Rahnamoun, Homa, Anand, Disha, Marinaccio, Christian, Hatton, Charlie, Wen, Yanhe, Stone, Richard M., Schaller, David, Mowla, Shoron, Xiao, Wenbin, Gamlen, Holly A., Stonestrom, Aaron J., Persaud, Sonali, Ener, Elizabeth, Cutler, Jevon A., Doench, John G., McGeehan, Gerard M., Volkamer, Andrea, Chodera, John D., Nowak, Radosław P., Fischer, Eric S., Levine, Ross L., Armstrong, Scott A., Cai, Sheng F.
Published in Nature (London) (30.03.2023)
Published in Nature (London) (30.03.2023)
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INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors
Li, Qing, Jiang, Baishan, Guo, Jiaye, Shao, Hong, Del Priore, Isabella S, Chang, Qing, Kudo, Rei, Li, Zhiqiang, Razavi, Pedram, Liu, Bo, Boghossian, Andrew S, Rees, Matthew G, Ronan, Melissa M, Roth, Jennifer A, Donovan, Katherine A, Palafox, Marta, Reis-Filho, Jorge S, de Stanchina, Elisa, Fischer, Eric S, Rosen, Neal, Serra, Violeta, Koff, Andrew, Chodera, John D, Gray, Nathanael S, Chandarlapaty, Sarat
Published in Cancer discovery (01.02.2022)
Published in Cancer discovery (01.02.2022)
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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo
Gill, Samuel C, Lim, Nathan M, Grinaway, Patrick B, Rustenburg, Ariën S, Fass, Josh, Ross, Gregory A, Chodera, John D, Mobley, David L
Published in The journal of physical chemistry. B (31.05.2018)
Published in The journal of physical chemistry. B (31.05.2018)
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