Zobrazeno 1 - 10
of 22
pro vyhledávání: '"Rafal P Wiewiora"'
Autor:
Dajun Sang, Sudarshan Pinglay, Rafal P Wiewiora, Myvizhi E Selvan, Hua Jane Lou, John D Chodera, Benjamin E Turk, Zeynep H Gümüş, Liam J Holt
Publikováno v:
eLife, Vol 8 (2019)
Protein kinases are crucial to coordinate cellular decisions and therefore their activities are strictly regulated. Previously we used ancestral reconstruction to determine how CMGC group kinase specificity evolved (Howard et al., 2014). In the prese
Externí odkaz:
https://doaj.org/article/cf1238b4c14c4d008114e3f1e72dbd96
Autor:
Shi Chen, Rafal P Wiewiora, Fanwang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fabio Pittella-Silva, Kyle A Beauchamp, Wolfram Tempel, Hualiang Jiang, Kaixian Chen, Robert J Skene, Yujun George Zheng, Peter J Brown, Jian Jin, Cheng Luo, John D Chodera, Minkui Luo
Publikováno v:
eLife, Vol 8 (2019)
Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate thes
Externí odkaz:
https://doaj.org/article/a6d43dbd70b84f88920fbdbf903ea4a3
Autor:
Yunrui Qiu, Rafal P. Wiewiora, Jesus A. Izaguirre, Huafeng Xu, Woody Sherman, Weiping Tang, Xuhui Huang
Publikováno v:
JACS Au, Vol 4, Iss 10, Pp 3857-3868 (2024)
Externí odkaz:
https://doaj.org/article/d4444b4550cf42629d07f9601298341b
Autor:
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks, Vijay S Pande
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features
Externí odkaz:
https://doaj.org/article/a3c536fb0ab14c8bbc0cb33e5bac84f0
Autor:
Sukrit Singh, Catherine E. Kuhn, Aoife M. Harbison, Vincent A. Voelz, John D. Chodera, Justin R. Porter, Neha Vithani, Joseph E. Coffland, Rafal P. Wiewiora, Artur Meller, Carl A Fogarty, Maxwell I. Zimmerman, Jonathan H. Borowsky, Gregory R. Bowman, Michael D. Ward, Matthew F. D. Hurley, Elisa Fadda, Upasana L. Mallimadugula
Publikováno v:
Nature Chemistry. 13:651-659
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression and replication that depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about thei
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::616c72101f8be9aa1b5000974b96797a
https://doi.org/10.1038/s41557-021-00707-0
https://doi.org/10.1038/s41557-021-00707-0
Autor:
Frank Noé, Christoph Wehmeyer, John D. Chodera, Daniel M. Zuckerman, Ernesto Suárez, Rafal P. Wiewiora
Publikováno v:
Journal of Chemical Theory and Computation
J Chem Theory Comput
J Chem Theory Comput
Markov state models (MSMs) have been widely applied to study the kinetics and pathways of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) simulations. These MSMs coarse-grain both configuration space and time
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::39424a17dd1b77ec46425cd62939559d
https://doi.org/10.1021/acs.jctc.0c01154
https://doi.org/10.1021/acs.jctc.0c01154
Autor:
Tandrila Das, Tao Peng, Hwayoung Lee, Howard C. Hang, Shibani Bhattacharya, Yumeng Li, Wonpil Im, Avital Percher, Emma H. Garst, Rafal P. Wiewiora, Isaac P. Witte
Publikováno v:
ACS Chem Biol
Interferon-induced transmembrane proteins (IFITMs) are S-palmitoylated proteins in vertebrates that restrict a diverse range of viruses. S-palmitoylated IFITM3 in particular engages incoming virus particles, prevents their cytoplasmic entry, and acce
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b052c254e193885b3a26d601eaf1eaf
https://doi.org/10.1021/acschembio.1c00013
https://doi.org/10.1021/acschembio.1c00013
Autor:
Christoph Wehmeyer, Frank Noé, John D. Chodera, Daniel M. Zuckerman, Rafal P. Wiewiora, Ernesto Suárez
Markov state models (MSMs) have been widely applied to study the kinetics and pathways of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) simulations. These MSMs coarse-grain both configuration space and time
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::14d4d15ce0a1ee948e9881b05da94c94
https://doi.org/10.1101/2020.11.09.374496
https://doi.org/10.1101/2020.11.09.374496
Autor:
Emma H. Garst, Tandrila Das, Rafal P. Wiewiora, Isaac P. Witte, Wonpil Im, Avital Percher, Howard C. Hang, Michael Goger, Tao Peng, Hwayoung Lee, Shibani Bhattacharya, Yumeng Li
Interferon-induced transmembrane proteins (IFITMs) areS-palmitoylated proteins in vertebrates that restrict a diverse range of viruses.S-palmitoylated IFITM3 in particular directly engages incoming virus particles, prevents their cytoplasmic entry, a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::58f28e9be866499091c4bdfdf72b6fbe
https://doi.org/10.1101/2020.09.11.293324
https://doi.org/10.1101/2020.09.11.293324
Autor:
Sukrit Singh, Rafal P. Wiewiora, John D. Chodera, Upasana L. Mallimadugula, Aoife M. Harbison, Maxwell I. Zimmerman, Jonathan H. Borowsky, Vincent A. Voelz, Matthew F. D. Hurley, Neha Vithani, Carl A Fogarty, Elisa Fadda, Gregory R. Bowman, Catherine E. Kuhn, Justin R. Porter, Joseph E. Coffland, Michael D. Ward, Artur Meller
Publikováno v:
Nature chemistry
bioRxiv
article-version (status) pre
article-version (number) 1
bioRxiv
article-version (status) pre
article-version (number) 1
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::95257af65179851fa72f91112ad7fd25
https://pubmed.ncbi.nlm.nih.gov/34031561
https://pubmed.ncbi.nlm.nih.gov/34031561