The development of an affinity evaluation and prediction system by using protein–protein docking simulations and parameter tuning

Autor: Koki Tsukamoto, Tatsuya Yoshikawa, Kiyonobu Yokota, Yuichiro Hourai, Kazuhiko Fukui

Publikováno v: Advances and Applications in Bioinformatics and Chemistry, Vol 2009, Iss default, Pp 1-15 (2009)

Koki Tsukamoto1, Tatsuya Yoshikawa1,2, Kiyonobu Yokota1, Yuichiro Hourai1, Kazuhiko Fukui11Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan; 2Department of Bi

Externí odkaz: https://doaj.org/article/8766f92aa88f4b0ba8b40511263f85b1

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Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality

Autor: Glen E. Kellogg, Hardik I. Parikh

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 82:916-932

Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::30e96d46e3886bbcf97f153db2a3dc05
https://doi.org/10.1002/prot.24466

The development of an affinity evaluation and prediction system by using protein–protein docking simulations and parameter tuning

Autor: Kazuhiko Fukui, Kiyonobu Yokota, Tatsuya Yoshikawa, Koki Tsukamoto, Yuichiro Hourai

Publikováno v: Advances and applications in bioinformatics and chemistry : AABC
Advances and Applications in Bioinformatics and Chemistry, Vol 2009, Iss default, Pp 1-15 (2009)

Koki Tsukamoto1, Tatsuya Yoshikawa1,2, Kiyonobu Yokota1, Yuichiro Hourai1, Kazuhiko Fukui11Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan; 2Department of Bi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c4cb7fb7871fd19470925e454f4136d8
https://www.dovepress.com/the-development-of-an-affinity-evaluation-and-prediction-system-by-usi-peer-reviewed-article-AABC

Screened charge electrostatic model in protein-protein docking simulations

Autor: Ruben Abagyan, Juan Fernández-Recio, Maxim Totrov

Publikováno v: Scopus-Elsevier
Europe PubMed Central
Pacific Symposium on Biocomputing

A new method for considering solvation when calculating electrostatics for protein docking is proposed. The solvent-exposed charges are attenuated by induced solvent polarization charges. Modified charges are pre-calculated and the correction doesn't

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3690afc48ed84dfbc5eb9893783e1f52
https://pubmed.ncbi.nlm.nih.gov/11928507