"http://www.isvav.cz/projectDetail.do?rowId=LH11020"^^ . . "0"^^ . . " ab initio methods" . "1"^^ . . . "0"^^ . . "molecular dynamics; ab initio methods; Potential energy surface (PES); conformation space; empirical potentials; peptides; proteins; structural database; peptide design"@en . "molecular dynamics" . "C\u00EDlem projektu je aplikace p\u0159esn\u00FDch v\u00FDpo\u010Dt\u016F pomoc\u00ED pokro\u010Dil\u00FDch metod kvantov\u00E9 chemie do empirick\u00FDch potenci\u00E1l\u016F pou\u017E\u00EDvan\u00FDch k popisu dynamick\u00E9ho chov\u00E1n\u00ED biomolekul, v na\u0161em p\u0159\u00EDpad\u011B peptid\u016F a protein\u016F. P\u016Fvodnost a unik\u00E1tnost projektu je v tom, \u017Ee s p\u0159esn\u00FDm popisem plochy potenci\u00E1ln\u00ED energie aminokyseliny v jej\u00EDm strukturn\u00EDm kontextu se m\u011Bn\u00ED n\u00E1sledn\u011B i dynamick\u00E9 chov\u00E1n\u00ED molekuly a to sm\u011Brem k podstatn\u011B lep\u0161\u00ED shod\u011B s experiment\u00E1ln\u00EDmi v\u00FDsledky z\u00EDskan\u00FDmi metodami NMR nebo infra\u010Dervenou spektroskopi\u00ED. To m\u00E1 z\u00E1sadn\u00ED v\u00FDznam pro studium jak protein\u016F maj\u00EDc\u00EDch strukturu tak p\u0159edev\u0161\u00EDm pro studium peptid\u016F a protein\u016F existuj\u00EDc\u00EDch jako nestrukturovan\u00E9. Jedn\u00EDm z v\u00FDstup\u016F je molekul\u00E1rn\u00ED design peptid\u016F pro supramolekul\u00E1rn\u00ED kompozice. 1. rok prob\u011Bhnou v\u00FDpo\u010Dty na vybran\u00E9 sad\u011B peptid\u016F a korekce pro empirick\u00FD potenci\u00E1l se aplikuje do potenci\u00E1lu. 2. rok se tato korekce otestuje na s\u00E9rii peptid\u016F a porovn\u00E1 s klasick\u00FDmi potenci\u00E1ly a experimentem. F\u00E1ze v\u00FDpo\u010Dt\u016F se 3.rok bude p\u0159ekr\u00FDvat s intenzivn\u00EDmi MD simulacemi a designem." . "2011-03-01+01:00"^^ . . " peptides" . " Potential energy surface (PES)" . "10"^^ . . "2014-12-31+01:00"^^ . . "10"^^ . " empirical potentials" . " structural database" . . . "Systematick\u00E9 mapov\u00E1n\u00ED konforma\u010Dn\u00EDho prostoru kr\u00E1tk\u00FDch peptid\u016F pomoc\u00ED v\u00FDpo\u010Detn\u00EDch metod - cesta k porozum\u011Bn\u00ED struktury protein\u016F a jejich sbalov\u00E1n\u00ED." . . "Systematic mapping of the conformational space of short peptides through molecular dynamics simulation - a way to understanding of protein structure formation."@en . . . "LH11020" . . . . . " conformation space" . . "2013-03-06+01:00"^^ . " proteins" . . "2015-02-16+01:00"^^ . "The aim of the project lies in systematic computational study (molecular dynamics) and consequent structural analysis of short peptides X-Y, X-Y-X and X-X-Y-X-X where X and Y means one of 20 L-amino acids composing proteins. The calculations will be based on the knowledge of the accurate ab initio potential energy surface in phi/psi torsional coordinates of an amino acid in sequence context. This should serve as the reference for two dimensional fit of the potential energy surface obtained by an empirical potential method. The parameters of the fit will be integrated into torsional term in the empirical force field functional form and free energy surfaces of peptides in water by means of molecular dynamics will be calculated. The results should serve as a reference for comparison with analysis made on corresponding peptides extracted from protein data bank. Statistical occurrences and minima position will be compared and analyzed."@en .