"Protein-protein interactions from molecular simulations"@en . . "7AMB15AT029" . . . . . "http://www.isvav.cz/projectDetail.do?rowId=7AMB15AT029"^^ . . "1. Metoda fitov\u00E1n\u00ED t\u0159et\u00EDho stupn\u011B s jednokrokovou pertubac\u00ED bude roz\u0161\u00ED\u0159ena tak, aby se mohla b\u011B\u017En\u011B pou\u017E\u00EDvat k v\u00FDpo\u010Dtu referen\u010Dn\u00EDch stav\u016F v\u0161ech aminokyselin, co\u017E zna\u010Dn\u011B zjednodu\u0161\u00ED v\u00FDpo\u010Detn\u00ED studium proteinov\u00FDch mutac\u00ED. Metoda bude testov\u00E1na na interakc\u00EDch mezi 14-3-3 proteiny a r\u016Fzn\u00FDmi fosforylovan\u00FDmi peptidy, konkr\u00E9tn\u011B pak p\u0159i studiu z\u00E1vislosti lok\u00E1ln\u00EDch zm\u011Bn v aminokyselinov\u00E9 sekvenci na afinit\u011B peptid\u016F k proteinu. 2. Metoda H-REMD s vyu\u017Eit\u00EDm r\u016Fzn\u00FDch parametr\u016F, tzv. distance field restraints, bude d\u00E1le vyv\u00EDjena za \u00FA\u010Delem p\u0159esn\u00E9ho popisu protein-peptidov\u00FDch a protein-proteinov\u00FDch interakc\u00ED. Velikost a flexibilita vazebn\u00E9ho ligandu zvy\u0161uje m\u00EDru vzorkov\u00E1n\u00ED, kter\u00E9 je nutn\u00E9 pro popis syst\u00E9mu. Na\u0161im c\u00EDlem tedy bude zlep\u0161en\u00ED popisu reak\u010Dn\u00ED koordin\u00E1ty. Tyto nov\u00E9 metody budou aplikov\u00E1ny na koopera\u010Dn\u00ED vazbu fosforylovan\u00FDch peptid\u016F ke 14-3-3 proteinu." . . . "2015-05-28+02:00"^^ . "1. The third-power fitting with one-step perturbation approach will be extended to define universal reference states for all amino acids, to facilitate a computational saturation mutagenesis experiments. Its applicability will be shown at the hand of the interaction between the 14-3-3 protein and various phosphorylated peptides, studying the effect of local changes in the sequence on the affinity of the peptides for the protein. 2. H-REMD using distancefield restraints will be further developed to allow for an accurate description of protein-peptide and protein-protein interactions. The size and flexibility of a ligand will increase the amount of sampling that is required and will need improvements in the description of the reaction coordinate. These new methodologies will be applied to the (cooperative) binding of phosphorylated peptides to the 14-3-3 protein."@en . "2015-01-01+01:00"^^ . . . "REMD, free energy, 14-3-3"@en . . "Studium protein-proteinov\u00FDch interakc\u00ED pomoc\u00ED molekul\u00E1rn\u00EDch simulac\u00ED" . . "1"^^ . "0"^^ . . "0"^^ . . . . . "0"^^ . . "0"^^ . . "2016-12-31+01:00"^^ . " free energy" . "REMD" .