Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Tami J. Marrone"'
Publikováno v:
Journal of Computational Chemistry. 18:1750-1759
We apply a combination of stochastic dynamics and Monte Carlo methods (MC/SD) to alanine dipeptide, with solvation forces derived from a Poisson–Boltzmann model supplemented with apolar terms. Our purpose is to study the effects of the model parame
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2f27c36bdca71ab56adb7054fd946b40
https://doi.org/10.1002/(sici)1096-987x(19971115)18:14<1750::aid-jcc4>3.0.co
https://doi.org/10.1002/(sici)1096-987x(19971115)18:14<1750::aid-jcc4>3.0.co
Autor:
Tami J. Marrone, J. Andrew McCammon,‡ and, André Collet, † Jeanne Costante-Crassous, James M. Briggs
Publikováno v:
Journal of the American Chemical Society. 119:3818-3823
Earlier NMR experiments (Canceill et. al. J. Am. Chem. Soc. 1985, 107, 6993) have shown that the inclusion of bromochlorofluoromethane (CHFClBr) 1 within the cavity of (−)-cryptophane-C 2 in chloro...
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::94ebc50d3e00f8e2ecc51b2581522889
https://doi.org/10.1021/ja9701164
https://doi.org/10.1021/ja9701164
Publikováno v:
Annual Review of Pharmacology and Toxicology. 37:71-90
▪ Abstract Structure-based computational methods continue to enhance progress in the discovery and refinement of therapeutic agents. Several such methods and their applications are described. These include molecular visualization and molecular mode
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5046561a5d6f8ae112c8db903edd796
https://doi.org/10.1146/annurev.pharmtox.37.1.71
https://doi.org/10.1146/annurev.pharmtox.37.1.71
Publikováno v:
Biophysical Journal. 72(2):522-532
Studying the thermodynamics of biochemical association reactions at the microscopic level requires efficient sampling of the configurations of the reactants and solvent as a function of the reaction pathways. In most cases, the associating ligand and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a7bc829f2f30ac74e9676b933e065d55
Publikováno v:
Journal of Medicinal Chemistry. 39:277-284
Molecular dynamics and free energy simulations were performed to examine the binding of (8R)-deoxycoformycin and (8R)-coformycin to adenosine deaminase. The two inhibitors differ only at the 2' position of the sugar ring ; the sugar moiety of conform
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18ccd61b3772e023968710efad1763bc
https://doi.org/10.1021/jm9505674
https://doi.org/10.1021/jm9505674
Autor:
Kenneth M. Merz, Tami J. Marrone
Publikováno v:
Journal of the American Chemical Society. 117:779-791
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::72f45694e40d1e86330f1493133f1788
https://doi.org/10.1021/ja00107a022
https://doi.org/10.1021/ja00107a022
Autor:
Kenneth M. Merz, Tami J. Marrone
Publikováno v:
The Journal of Physical Chemistry. 97:6524-6529
Parameters were derived empirically for K + and Na + that qualitatively reproduce the absolute free energise of solvation and structural characteristics of these ions in methanol. The procedure used free energy perturbation simulations to obtain the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::85ad7b05aabb41d84a8b14c600e94d4e
https://doi.org/10.1021/j100126a031
https://doi.org/10.1021/j100126a031
Autor:
Tami J. Marrone, Kenneth M. Merz
Publikováno v:
Journal of the American Chemical Society. 114:7542-7549
Potential of mean force (PMF), free energy perturbation (FEP), and molecular dynamics (MD) computer simulations have been used to investigate the molecular recognition of K + by the ionophore nonactin in methanol. First, parameter sets for K + and Na
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::248f39881aeeede8cb8fc9c32d1cd066
https://doi.org/10.1021/ja00045a030
https://doi.org/10.1021/ja00045a030
Publikováno v:
The Journal of Physical Chemistry. 100:1439-1441
We compute the potential of mean force (PMF) around the φ and ψ torsions of alanine dipeptide with a Poisson−Boltzmann (PB) method and compare these results to simulations in explicit water. The PB method, which includes an apolar solvation term,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::459a8c98f221da9f09cdee174f4b2783
https://doi.org/10.1021/jp952835f
https://doi.org/10.1021/jp952835f
Publikováno v:
The Journal of Physical Chemistry. 98:1341-1343
We present a method to calculate the charge redistribution that occurs during ionophore potential of mean force (PMF) calculations. A new charge distribution is calculated at the beginning of each simulation that is used to assemble the PMF energy pr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a4aa8df9d88a7d32e5941880c35f1f82
https://doi.org/10.1021/j100055a048
https://doi.org/10.1021/j100055a048