Zobrazeno 1 - 10
of 35
pro vyhledávání: '"Daniel R. Roe"'
Autor:
Daniel R. Roe, Bernard R. Brooks
Publikováno v:
Protein science : a publication of the Protein Society. 31(12)
Molecular dynamics (MD) simulations are now able to routinely reach timescales of microseconds and beyond. This has led to a corresponding increase in the amount of MD trajectory data that needs to be stored, particularly when those trajectories cont
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::933cec18788f58182b70924bde978906
https://pubmed.ncbi.nlm.nih.gov/36382864
https://pubmed.ncbi.nlm.nih.gov/36382864
Autor:
Ana Damjanović, Xiongwu Wu, Daniel R. Roe, Ada Y. Chen, Bernard R. Brooks, Robert L Rosenberg
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 88:527-539
The selectivity filter (SF) of bacterial voltage-gated sodium channels consists of four glutamate residues arranged in a C4 symmetry. The protonation state population of this tetrad is unclear. To address this question, we simulate the pore domain of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86036f05faeaf753477212c04e6182e9
https://doi.org/10.1002/prot.25831
https://doi.org/10.1002/prot.25831
Autor:
Andrew C. Simmonett, Nanjie Deng, Daniel R. Roe, Lieyang Chen, Anthony Cruz, Tom Kurtzman, Lauren Wickstrom
Publikováno v:
J Chem Theory Comput
Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range non-bonded i
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::93b66ed65f60e29117f95f6a92944ccc
https://doi.org/10.26434/chemrxiv.13140011.v1
https://doi.org/10.26434/chemrxiv.13140011.v1
Autor:
Daniel R. Roe, Bernard R. Brooks
Publikováno v:
J Chem Phys
Before beginning the production phase of molecular dynamics simulations, i.e., the phase that produces the data to be analyzed, it is often necessary to first perform a series of one or more preparatory minimizations and/or molecular dynamics simulat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::51c2629962bbe4ea0a27a9b336717b4e
https://pubmed.ncbi.nlm.nih.gov/32770927
https://pubmed.ncbi.nlm.nih.gov/32770927
Autor:
Hamed S. Hayatshahi, Rodrigo Galindo-Murillo, Thomas E. Cheatham, Daniel R. Roe, Kathleen B. Hall
Publikováno v:
The Journal of Physical Chemistry. B
An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although su
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::571b0f03b7dc9cbc944da0b62a2bc6e3
https://doi.org/10.1021/acs.jpcb.6b08764
https://doi.org/10.1021/acs.jpcb.6b08764
Autor:
Daniel R. Roe, Andrew J. Schultz, Daniel M. Zuckerman, Paul N. Patrone, Alan Grossfield, Daniel W. Siderius
Publikováno v:
Living Journal of Computational Molecular Science. 1
The quantitative assessment of uncertainty and sampling quality is essential in molecular simulation. Many systems of interest are highly complex, often at the edge of current computational capabilities. Modelers must therefore analyze and communicat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d08c662a84fdbbacf58a0f96966708c
https://doi.org/10.33011/livecoms.1.1.5067
https://doi.org/10.33011/livecoms.1.1.5067
Publikováno v:
Languages and Compilers for Parallel Computing ISBN: 9783030352240
LCPC
LCPC
This paper reveals challenges in migrating C++ codes to GPUs using polyhedral compiler technology. We point to instances where reasoning about C++ constructs in a polyhedral model is feasible. We describe a case study using CPPTRAJ, an analysis code
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e5514ed4002898943e72d27e74b7b88e
https://doi.org/10.1007/978-3-030-35225-7_3
https://doi.org/10.1007/978-3-030-35225-7_3
Autor:
Daniel R. Roe, Bernard R. Brooks
Publikováno v:
J Mol Graph Model
Visualizing data generated from molecular dynamics simulations can be difficult, particularly when there can be thousands to millions of trajectory frames. The creation of a 3D grid of atomic density (i.e. a volumetric map) is one way to easily view
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ee58ffac83194e7f375c71233f1d115f
https://doi.org/10.1016/j.jmgm.2021.107832
https://doi.org/10.1016/j.jmgm.2021.107832
Autor:
Thomas E. Cheatham, Elizabeth Pierce, Vinayak Agarwal, Satish K. Nair, John A. McIntosh, Yue Hao, Daniel R. Roe, Maho Morita, Eric W. Schmidt
Publikováno v:
Proceedings of the National Academy of Sciences. 113:14037-14042
The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tole
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e3a8faf14a7dc1e7ff5e45a8159d31bd
https://doi.org/10.1073/pnas.1609869113
https://doi.org/10.1073/pnas.1609869113
Publikováno v:
Journal of Chemical Information and Modeling. 56:1282-1291
Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. T
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5ede54fd18abea31c21db01ea97d785c
https://doi.org/10.1021/acs.jcim.5b00727
https://doi.org/10.1021/acs.jcim.5b00727