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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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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Journal Article
STORMM: Structure and topology replica molecular mechanics for chemical simulations
Cerutti, David S., Wiewiora, Rafal, Boothroyd, Simon, Sherman, Woody
Published in The Journal of chemical physics (21.07.2024)
Published in The Journal of chemical physics (21.07.2024)
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Molecular Latent Space Simulators for Distributed and Multimolecular Trajectories
Jones, Michael S., McDargh, Zachary A., Wiewiora, Rafal P., Izaguirre, Jesus A., Xu, Huafeng, Ferguson, Andrew L.
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (29.06.2023)
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (29.06.2023)
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What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models
Suárez, Ernesto, Wiewiora, Rafal P, Wehmeyer, Chris, Noé, Frank, Chodera, John D, Zuckerman, Daniel M
Published in Journal of chemical theory and computation (11.05.2021)
Published in Journal of chemical theory and computation (11.05.2021)
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Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity
Wright, Tom H., Bower, Ben J., Chalker, Justin M., Bernardes, Gonçalo J. L., Wiewiora, Rafel, Ng, Wai-Lung, Raj, Ritu, Faulkner, Sarah, Vallée, M. Robert J., Phanumartwiwath, Anuchit, Coleman, Oliver D., Thézénas, Marie-Laëtitia, Khan, Maola, Galan, Sébastien R. G., Lercher, Lukas, Schombs, Matthew W., Gerstberger, Stefanie, Palm-Espling, Maria E., Baldwin, Andrew J., Kessler, Benedikt M., Claridge, Timothy D. W., Mohammed, Shabaz, Davis, Benjamin G.
Published in Science (American Association for the Advancement of Science) (04.11.2016)
Published in Science (American Association for the Advancement of Science) (04.11.2016)
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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
Dixon, Tom, MacPherson, Derek, Mostofian, Barmak, Dauzhenka, Taras, Lotz, Samuel, McGee, Dwight, Shechter, Sharon, Shrestha, Utsab R., Wiewiora, Rafal, McDargh, Zachary A., Pei, Fen, Pal, Rajat, Ribeiro, João V., Wilkerson, Tanner, Sachdeva, Vipin, Gao, Ning, Jain, Shourya, Sparks, Samuel, Li, Yunxing, Vinitsky, Alexander, Zhang, Xin, Razavi, Asghar M., Kolossváry, István, Imbriglio, Jason, Evdokimov, Artem, Bergeron, Louise, Zhou, Wenchang, Adhikari, Jagat, Ruprecht, Benjamin, Dickson, Alex, Xu, Huafeng, Sherman, Woody, Izaguirre, Jesus A.
Published in Nature communications (06.10.2022)
Published in Nature communications (06.10.2022)
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Journal Article
The dynamic conformational landscape of the protein methyltransferase SETD8
Chen, Shi, Wiewiora, Rafal P, Meng, Fanwang, Babault, Nicolas, Ma, Anqi, Yu, Wenyu, Qian, Kun, Hu, Hao, Zou, Hua, Wang, Junyi, Fan, Shijie, Blum, Gil, Pittella-Silva, Fabio, Beauchamp, Kyle A, Tempel, Wolfram, Jiang, Hualiang, Chen, Kaixian, Skene, Robert J, Zheng, Yujun George, Brown, Peter J, Jin, Jian, Luo, Cheng, Chodera, John D, Luo, Minkui
Published in eLife (13.05.2019)
Published in eLife (13.05.2019)
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Ancestral reconstruction reveals mechanisms of ERK regulatory evolution
Sang, Dajun, Pinglay, Sudarshan, Wiewiora, Rafal P, Selvan, Myvizhi E, Lou, Hua Jane, Chodera, John D, Turk, Benjamin E, Gümüş, Zeynep H, Holt, Liam J
Published in eLife (13.08.2019)
Published in eLife (13.08.2019)
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Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems
Gkeka, Paraskevi, Stoltz, Gabriel, Barati Farimani, Amir, Belkacemi, Zineb, Ceriotti, Michele, Chodera, John D, Dinner, Aaron R, Ferguson, Andrew L, Maillet, Jean-Bernard, Minoux, Hervé, Peter, Christine, Pietrucci, Fabio, Silveira, Ana, Tkatchenko, Alexandre, Trstanova, Zofia, Wiewiora, Rafal, Lelièvre, Tony
Published in Journal of chemical theory and computation (11.08.2020)
Published in Journal of chemical theory and computation (11.08.2020)
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Site-Specific Lipidation Enhances IFITM3 Membrane Interactions and Antiviral Activity
Garst, Emma H, Lee, Hwayoung, Das, Tandrila, Bhattacharya, Shibani, Percher, Avital, Wiewiora, Rafal, Witte, Isaac P, Li, Yumeng, Peng, Tao, Im, Wonpil, Hang, Howard C
Published in ACS chemical biology (21.05.2021)
Published in ACS chemical biology (21.05.2021)
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Journal Article
SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal 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 bioRxiv (07.10.2020)
Published in bioRxiv (07.10.2020)
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Paper
SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal 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 (24.05.2021)
Published in Nature chemistry (24.05.2021)
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An efficient one-pot synthesis of 2-bromo-6-aryl[5H]pyrrolo[2,3-b]pyrazines
Simpson, Iain, St-Gallay, Steve A., Stokes, Stephen, Whittaker, David T.E., Wiewiora, Rafal
Published in Tetrahedron letters (18.03.2015)
Published in Tetrahedron letters (18.03.2015)
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Journal Article
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
Gkeka, Paraskevi, Stoltz, Gabriel, Farimani, Amir Barati, Belkacemi, Zineb, Ceriotti, Michele, Chodera, John, Dinner, Aaron R, Ferguson, Andrew, Maillet, Jean-Bernard, Minoux, Hervé, Peter, Christine, Pietrucci, Fabio, Silveira, Ana, Tkatchenko, Alexandre, Trstanova, Zofia, Wiewiora, Rafal, Leliévre, Tony
Year of Publication 15.04.2020
Year of Publication 15.04.2020
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