2007
Program for Analysis of Internal Motion in Molecular Dynamics Simulation
NOVÁK, Petr; Lukáš ŽÍDEK; Pavel MACEK; Petr PADRTA; Vladimír SKLENÁŘ et al.Základní údaje
Originální název
Program for Analysis of Internal Motion in Molecular Dynamics Simulation
Název česky
Program pro analýzu vnitřních pohybů v molekulové dynamice
Autoři
NOVÁK, Petr; Lukáš ŽÍDEK; Pavel MACEK; Petr PADRTA a Vladimír SKLENÁŘ
Vydání
Brno, Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul" 1 s. 2007
Nakladatel
Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta
Další údaje
Jazyk
angličtina
Typ výsledku
Stať ve sborníku
Obor
10403 Physical chemistry
Stát vydavatele
Česká republika
Utajení
není předmětem státního či obchodního tajemství
Označené pro přenos do RIV
Ne
Organizační jednotka
Přírodovědecká fakulta
Klíčová slova anglicky
MD; PAIN; protein; dynamics;
Příznaky
Mezinárodní význam
Změněno: 9. 4. 2010 13:44, prof. Mgr. Lukáš Žídek, Ph.D.
V originále
Molecular dynamics (MD) simulations of the proteins provide us huge amount of data describing coordinates of all atoms and their changes in course of time. This enables us to extract motional parameters of the studied molecule. For this purpose the program PAIN (Program for Analysis of Internal motioN) was written. It is written in C language so that the analysis of large amount of data is fairly fast and it should be rather easily portable on the majority of the current platforms. Some key features implemented in PAIN up to date are calculation of the : * correlation function of the vector * generalized order parameter * frequency dependent generalized order parameter * conformation dependent generalized order parameter * spatial distribution of the internuclear vector orientations * histogram of the dihedral angle (including number of modes and distribution parameters estimation) * conformation transitions analysis Program was tested on and used for an analysis of the MD simulation of the mouse Major Urinary Protein-I in an explicit solvent.
Česky
Molecular dynamics (MD) simulations of the proteins provide us huge amount of data describing coordinates of all atoms and their changes in course of time. This enables us to extract motional parameters of the studied molecule. For this purpose the program PAIN (Program for Analysis of Internal motioN) was written. It is written in C language so that the analysis of large amount of data is fairly fast and it should be rather easily portable on the majority of the current platforms. Some key features implemented in PAIN up to date are calculation of the : * correlation function of the vector * generalized order parameter * frequency dependent generalized order parameter * conformation dependent generalized order parameter * spatial distribution of the internuclear vector orientations * histogram of the dihedral angle (including number of modes and distribution parameters estimation) * conformation transitions analysis Program was tested on and used for an analysis of the MD simulation of the mouse Major Urinary Protein-I in an explicit solvent.
Návaznosti
| GD204/03/H016, projekt VaV |
| ||
| MSM0021622413, záměr |
|