Zobrazeno 1 - 10
of 643
pro vyhledávání: '"Karl F. Freed"'
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 12, p e1006342 (2018)
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we present a rapid self-consistent approximation of the side chain free energy at every integration st
Externí odkaz:
https://doaj.org/article/acc06078665e4c9c936a64fc59eefd0b
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 12, p e1006578 (2018)
An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics. The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assump
Externí odkaz:
https://doaj.org/article/77024e231a02488287694c95dea0776d
Publikováno v:
Journal of Chemical Theory and Computation. 18:2016-2032
Predicting protein binding is a core problem of computational biophysics. That this objective can be partly achieved with some amount of success using docking algorithms based on rigid protein models is remarkable, although going further requires all
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3bb6d95d14ac3810b99a9797079c954
https://doi.org/10.1021/acs.jctc.1c01255
https://doi.org/10.1021/acs.jctc.1c01255
Publikováno v:
ACS macro letters. 5(12)
Numerous experiments reveal that the dynamics of glass-forming polymer melts are profoundly influenced by the application of pressure, but a fundamental microscopic understanding of these observations remains incomplete. We explore the structural rel
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::179b52844db88fb70276496202deced3
https://pubmed.ncbi.nlm.nih.gov/35651209
https://pubmed.ncbi.nlm.nih.gov/35651209
Publikováno v:
ACS macro letters. 1(1)
Increasing the molar mass of the polymers in blends and in solutions tends to decrease miscibility, but application of the lattice cluster theory for strongly interactiong polymer systems to telechelic polymer solutions explains why this usual trend
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::12e0db9222b9f55625547a1fa2f37f7f
https://pubmed.ncbi.nlm.nih.gov/35578460
https://pubmed.ncbi.nlm.nih.gov/35578460
Autor:
Sachin R. Natesh, Esmael J. Haddadian, Stephen C. Meredith, Tobin R. Sosnick, Jack F. Douglas, Karl F. Freed, A. R. Hummels, Joseph R. Sachleben
Publikováno v:
J Chem Phys
We compared all-atom explicit solvent molecular dynamics simulations of three types of Aβ(1–40) fibrils: brain-seeded fibrils (2M4J, with a threefold axial symmetry) and the other two, all-synthetic fibril polymorphs (2LMN and 2LMP, made under dif
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::683c37acd59c163a09e622c7ee2253b4
https://europepmc.org/articles/PMC8214467/
https://europepmc.org/articles/PMC8214467/
Publikováno v:
PLoS ONE, Vol 7, Iss 2, p e32647 (2012)
We consider the identification of interacting protein-nucleic acid partners using the rigid body docking method FTdock, which is systematic and exhaustive in the exploration of docking conformations. The accuracy of rigid body docking methods is test
Externí odkaz:
https://doaj.org/article/14f970e67c46408287dff22342fe7ccd
Autor:
Karl F. Freed, John M. Jumper, Adam M. Zmyslowski, Micayla A. Bowman, Tobin R. Sosnick, Emily B. Kaye, Joshua A. Riback, James R. Hinshaw, Catherine R. Knoverek, Patricia L. Clark
Publikováno v:
Science
An expanded view of disordered proteins Disordered proteins sample an ensemble of conformations, but it has remained unclear how compact these conformations are in water. Polymer physics relates the radius of gyration ( R g ) to solvent quality, with
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::15bac96d64670b9e2188a08b9424e476
https://doi.org/10.1126/science.aan5774
https://doi.org/10.1126/science.aan5774
Publikováno v:
Macromolecules. 50:2585-2598
We investigate the thermodynamic and dynamic properties of a model unentangled glass-forming polymer melt over a wide range of pressures (P) and temperatures (T) using molecular dynamics simulation. We show that the T dependence of the reduced therma
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::27a2ca99cae9573dbf7c8b9a9c57ce72
https://doi.org/10.1021/acs.macromol.7b00080
https://doi.org/10.1021/acs.macromol.7b00080
On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations
Publikováno v:
Biophys J
Single-molecule force spectroscopy has proven extremely beneficial in elucidating folding pathways for membrane proteins. Here, we simulate these measurements, conducting hundreds of unfolding trajectories using our fast Upside algorithm for slow eno
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9c446d18d906870a4771349971e01a46
https://pubmed.ncbi.nlm.nih.gov/31587831
https://pubmed.ncbi.nlm.nih.gov/31587831