Výsledky vyhledávání - "John P. Cvitkovic"

Expansion and Additional Validation of PKA17: A Fast Real-Time and Web-Based pKa Predictor

Autor: Connor D. Pauplis, George A. Kaminski, John P. Cvitkovic, Phoebe C. Carney

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

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PKA17—A Coarse‐Grain Grid‐Based Methodology and Web‐Based Software for Predicting Protein p K a Shifts

Autor: John P. Cvitkovic, George A. Kaminski, Connor D. Pauplis

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

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PKA17-A Coarse-Grain Grid-Based Methodology and Web-Based Software for Predicting Protein pK

Autor: John P, Cvitkovic, Connor D, Pauplis, George A, Kaminski

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

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Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione through the Formation of Metal-Sulfur Clusters

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

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POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins

Autor: Sergei Y. Ponomarev, John P. Cvitkovic, George A. Kaminski, Xinbi Li, Daniel L. Sigalovsky

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

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Developing multisite empirical force field models for Pt(II) and cisplatin

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

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