Zobrazeno 1 - 10
of 12
pro vyhledávání: '"Ali S Saglam"'
Autor:
Adam Husar, Mariam Ordyan, Guadalupe C Garcia, Joel G Yancey, Ali S Saglam, James R Faeder, Thomas M Bartol, Mary B Kennedy, Terrence J Sejnowski
Publikováno v:
PLoS Computational Biology, Vol 20, Iss 4, p e1011800 (2024)
Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularit
Externí odkaz:
https://doaj.org/article/828622620d444e6f93288d60263aacac
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:
Adam Husar, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey, Ali S. Saglam, James R. Faeder, Thomas M. Bartol, Terrence J. Sejnowski
Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::614cf82110bc5cf2284c9de414bc2362
https://doi.org/10.1101/2022.05.17.492333
https://doi.org/10.1101/2022.05.17.492333
Autor:
Robin Schmucker, Gabriele Farina, Ali S. Saglam, Tuomas Sandholm, Fröhlich F, James R. Faeder
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 17, Iss 12, p e1009689 (2021)
PLoS Computational Biology, Vol 17, Iss 12, p e1009689 (2021)
The design of efficient combination therapies is a difficult key challenge in the treatment of complex diseases such as cancers. The large heterogeneity of cancers and the large number of available drugs renders exhaustive in vivo or even in vitro in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60dbab5fdb9dae135af5e9bd9dafb135
http://europepmc.org/articles/PMC8747684
http://europepmc.org/articles/PMC8747684
Autor:
Ali S. Saglam, Lillian T. Chong
Publikováno v:
Chemical Science
The weighted ensemble (WE) strategy enables direct simulation of atomistic, fully-continuous protein–protein binding pathways in explicit solvent, yielding rigorous kinetics.
A grand challenge in the field of biophysics has been the complete c
A grand challenge in the field of biophysics has been the complete c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e41b16956865bbab3a3a0bfa2afe0c44
https://doi.org/10.1039/c8sc04811h
https://doi.org/10.1039/c8sc04811h
Autor:
Jordan J A Weaver, Yafei Wang, Chase Cockrell, Michael Getz, Nicholson Collier, Caroline I Larkin, Padmini Rangamani, Sara Hamis, Amber M. Smith, Ashlee N. Ford Versypt, Courtney L. Davis, Jason E. Shoemaker, Bing Liu, Mohammad Aminul Islam, Ali S. Saglam, Andrew Becker, Penelope A. Morel, Tarunendu Mapder, Fiona R Macfarlane, Jonathan Ozik, Thomas Hillen, Dennis Hou, James R. Faeder, Gary An, Furkan Kurtoglu, Pablo Maygrundter, Juliano Ferrari Gianlupi, Maansi Asthana, James A. Glazier, Paul Macklin, Randy Heiland, Elsje Pienaar, Aarthi Narayanan, Adrianne L. Jenner, Morgan Craig
Publikováno v:
bioRxiv
The 2019 novel coronavirus, SARS-CoV-2, is a pathogen of critical significance to international public health. Knowledge of the interplay between molecular-scale virus-receptor interactions, single-cell viral replication, intracellular-scale viral tr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f4cc2f3702aeba3003fe54865d5935b0
https://doi.org/10.1101/2020.04.02.019075
https://doi.org/10.1101/2020.04.02.019075
Publikováno v:
The Journal of Physical Chemistry B. 121:10046-10054
Many intrinsically disordered proteins, which are prevalent in nature, fold only upon binding their structured partner proteins. Such proteins have been hypothesized to have a kinetic advantage over their folded, preorganized analogues in binding the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9bf04fac1177be2c60367501dc093a8d
https://doi.org/10.1021/acs.jpcb.7b08486
https://doi.org/10.1021/acs.jpcb.7b08486
Autor:
Jose-Juan Tapia, James R. Faeder, Jacob Czech, Thomas M. Bartol, Robert Kuczewski, Ali S. Saglam, Terrence J. Sejnowski
Publikováno v:
Modeling Biomolecular Site Dynamics ISBN: 9781493991006
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely used mode
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f90514206e45679ef91eba7f64e0c1e2
https://doi.org/10.1007/978-1-4939-9102-0_9
https://doi.org/10.1007/978-1-4939-9102-0_9
Autor:
Daniel M. Zuckerman, Paige O. Harrison, Anthony T. Bogetti, Joshua L. Adelman, Max F. Dudek, Upendra Adhikari, Paul A. Torrillo, Lillian T. Chong, Adam J. Pratt, Barmak Mostofian, Matthew C. Zwier, Ali S. Saglam, Alex Dickson, Alex J. DeGrave
Publikováno v:
Living J Comput Mol Sci
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present fiv
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4fe460d052ae315419a81fdaf27bd6b1
https://doi.org/10.33011/livecoms.1.2.10607
https://doi.org/10.33011/livecoms.1.2.10607
Autor:
Lillian T. Chong, Ali S. Saglam
A grand challenge in the field of biophysics has been the complete characterization of protein-protein binding processes at atomic resolution. This characterization requires the direct simulation of binding pathways starting from the initial unbound
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::85cb01b151905e67e2f786fd6529489c
https://doi.org/10.1101/453985
https://doi.org/10.1101/453985