Zobrazeno 1 - 10
of 42
pro vyhledávání: '"George A, Kaminski"'
Publikováno v:
Journal of Computational Biophysics and Chemistry. 22:207-218
In this paper, we report results of using molecular modeling to assign specific Zn(II) binding affinities to the known binding sites of the YiiP–zinc transporter. YiiP is a cation-diffusion facilitator. It facilitates the transmembrane exchange of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::756d2c1851b077d6f3a898ffd2f3d3cc
https://doi.org/10.1142/s2737416523500126
https://doi.org/10.1142/s2737416523500126
Publikováno v:
Journal of Computational Biophysics and Chemistry. 20:141-152
We have further improved and validated PKA17, our fast software for predicting p[Formula: see text] values of protein residues. The methodology employs coarse-grained lattice-based model of proteins. It was previously demonstrated to perform ca. an o
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::37fd992bc9517bb29de10f83292c8314
https://doi.org/10.1142/s273741652042003x
https://doi.org/10.1142/s273741652042003x
Publikováno v:
Journal of Computational Chemistry. 40:1718-1726
We have developed and tested PKA17, a coarse-grain grid-based model for predicting protein pK a shifts. Our pK a predictor is currently deployed via a website interface. We have carried out parameter fitting using 442 Asp, Glu, His, Lys, and Arg resi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8fc65d91287e31e1c9b94c3f84a9578b
https://doi.org/10.1002/jcc.25826
https://doi.org/10.1002/jcc.25826
Publikováno v:
Journal of computational chemistry. 40(18)
We have developed and tested PKA17, a coarse-grain grid-based model for predicting protein pK
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::02ee5894716d81b6751dc0c30f90047c
https://pubmed.ncbi.nlm.nih.gov/30895643
https://pubmed.ncbi.nlm.nih.gov/30895643
Autor:
George A. Kaminski, Ingrid J. Pickering, John P. Cvitkovic, Oleg Y. Dmitriev, Kelly L. Summers, Graham N. George, Kurt H. Nienaber, Corey H. Yu, Natalia V. Dolgova, Julien J. H. Cotelesage, Miroslav Hodak, Jerzy Bernholc
Publikováno v:
Biochemistry. 56(24)
Copper is an essential nutrient required for many biological processes involved in primary metabolism, but free copper is toxic due to its ability to catalyze formation of free radicals. To prevent toxic effects, in the cell copper is bound to protei
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4cba38e2eeed8a02c258ec8d7b9ceba3
https://pubmed.ncbi.nlm.nih.gov/28549213
https://pubmed.ncbi.nlm.nih.gov/28549213
Autor:
George A. Kaminski
Publikováno v:
Journal of Chemical Theory and Computation
We have simulated effects of a shock wave in water that would result from the collapse of a cavitation bubble on binding in model complexes. We have considered a benzene dimer, a pair of uracil molecules, a complex of fragments of the X-linked inhibi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5d77cad6a6986a4956ef4ef0c128702d
https://doi.org/10.1021/ct500461s
https://doi.org/10.1021/ct500461s
Publikováno v:
Journal of Chemical Theory and Computation
Previously, we reported development of a fast polarizable force field and software named POSSIM (POlarizable Simulations with Second order Interaction Model). The second-order approximation permits the speed up of the polarizable component of the cal
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd2b3967beb372c61f450f9ab49e5cac
http://europepmc.org/articles/PMC4230370
http://europepmc.org/articles/PMC4230370
Publikováno v:
Journal of Computational Chemistry. 34:1241-1250
A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6838843602088b84aad5c5ce2322461
https://doi.org/10.1002/jcc.23248
https://doi.org/10.1002/jcc.23248
Autor:
John P. Cvitkovic, George A. Kaminski
Publikováno v:
Journal of computational chemistry. 38(3)
We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used—modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create trans
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ced96a6ca70b50a8ecfc8500599e7944
https://pubmed.ncbi.nlm.nih.gov/27859392
https://pubmed.ncbi.nlm.nih.gov/27859392
Autor:
George A. Kaminski, Ity Sharma
Publikováno v:
Journal of computational chemistry. 38(2)
Our Fuzzy-Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second-order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6e8712295b27b30110484bcb5af20ba4
https://pubmed.ncbi.nlm.nih.gov/27785788
https://pubmed.ncbi.nlm.nih.gov/27785788