Zobrazeno 1 - 10
of 184
pro vyhledávání: '"Daniel M. Zuckerman"'
Publikováno v:
Communications Biology, Vol 6, Iss 1, Pp 1-12 (2023)
Abstract Time-lapse imaging is a powerful approach to gain insight into the dynamic responses of cells, but the quantitative analysis of morphological changes over time remains challenging. Here, we exploit the concept of “trajectory embedding” t
Externí odkaz:
https://doaj.org/article/c3cd13b8922241de89bb9f79380820f5
Autor:
Jonathan A. Flores, Bassam G. Haddad, Kimberly A. Dolan, Janette B. Myers, Craig C. Yoshioka, Jeremy Copperman, Daniel M. Zuckerman, Steve L. Reichow
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-11 (2020)
The local lipid environment is known to affect the structure, stability and intercellular channel activity of gap junctions, however, the molecular basis for these effects remains unknown. Here authors report the CryoEM structure of Cx46/50 lipid-emb
Externí odkaz:
https://doaj.org/article/cc52d1281bb34d24bc69004c93903dd8
Autor:
Yerim Lee, Carey Phelps, Tao Huang, Barmak Mostofian, Lei Wu, Ying Zhang, Kai Tao, Young Hwan Chang, Philip JS Stork, Joe W Gray, Daniel M Zuckerman, Xiaolin Nan
Publikováno v:
eLife, Vol 8 (2019)
Membrane nanodomains have been implicated in Ras signaling, but what these domains are and how they interact with Ras remain obscure. Here, using single particle tracking with photoactivated localization microscopy (spt-PALM) and detailed trajectory
Externí odkaz:
https://doaj.org/article/d27e8702f8fd47e69432bdeac6dc2cfc
Publikováno v:
Communications Biology. 6
Time-lapse imaging is a powerful approach to gain insight into the dynamic responses of cells, but the quantitative analysis of morphological changes over time remains challenging. Here, we exploit the concept of “trajectory embedding” to analyze
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4168e89c1e240bd676a2559524b8a2ab
https://doi.org/10.1038/s42003-023-04837-8
https://doi.org/10.1038/s42003-023-04837-8
Autor:
John D. Russo, She Zhang, Jeremy M. G. Leung, Anthony T. Bogetti, Jeff P. Thompson, Alex J. DeGrave, Paul A. Torrillo, A. J. Pratt, Kim F. Wong, Junchao Xia, Jeremy Copperman, Joshua L. Adelman, Matthew C. Zwier, David N. LeBard, Daniel M. Zuckerman, Lillian T. Chong
Publikováno v:
J Chem Theory Comput
The weighted ensemble (WE) family of methods is one of several statistical-mechanics based path sampling strategies that can provide estimates of key observables (rate constants, pathways) using a fraction of the time required by direct simulation me
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e390c6ced9ac98b6fa1d7028ed0b0a87
https://doi.org/10.1021/acs.jctc.1c01154
https://doi.org/10.1021/acs.jctc.1c01154
Autor:
Anthony T. Bogetti, Jeremy M. G. Leung, John D. Russo, She Zhang, Jeff P. Thompson, Ali S. Saglam, Dhiman Ray, Rhea C. Abraham, James R. Faeder, Ioan Andricioaei, Joshua L. Adelman, Matthew C. Zwier, David N. LeBard, Daniel M. Zuckerman, Lillian T. Chong
We present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensemble (WE) pa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c5823b98c7575c47bf7d377a5187b9db
https://doi.org/10.1101/2022.10.04.510803
https://doi.org/10.1101/2022.10.04.510803
Autor:
John D. Russo, Daniel M. Zuckerman
Publikováno v:
Biophysical Journal. 122:177a-178a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::cf378e120e043662d03d8a1ff59c20a5
https://doi.org/10.1016/j.bpj.2022.11.1102
https://doi.org/10.1016/j.bpj.2022.11.1102
Autor:
Won Hee Ryu, John Russo, Mats S. Johnson, Jeffrey P. Thompson, David N. LeBard, Gideon Simpson, David Aristoff, Robert J. Webber, Jeremy T. Copperman, Daniel M. Zuckerman
Publikováno v:
Biophysical Journal. 122:422a-423a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e8f5e94f3624e30d84deeeb0852574b3
https://doi.org/10.1016/j.bpj.2022.11.2289
https://doi.org/10.1016/j.bpj.2022.11.2289
Publikováno v:
PLoS ONE, Vol 12, Iss 3, p e0173500 (2017)
ATP-driven proton pumps, which are critical to the operation of a cell, maintain cytosolic and organellar pH levels within a narrow functional range. These pumps employ two very different mechanisms: an elaborate rotary mechanism used by V-ATPase H+
Externí odkaz:
https://doaj.org/article/8c0641a13617475d829f697e884b1fdc
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