Detailed Information on Publication Record
2007
Program for Analysis of Internal Motion in Molecular Dynamics Simulation
NOVÁK, Petr, Lukáš ŽÍDEK, Pavel MACEK, Petr PADRTA, Vladimír SKLENÁŘ et. al.Basic information
Original name
Program for Analysis of Internal Motion in Molecular Dynamics Simulation
Name in Czech
Program pro analýzu vnitřních pohybů v molekulové dynamice
Authors
NOVÁK, Petr, Lukáš ŽÍDEK, Pavel MACEK, Petr PADRTA and Vladimír SKLENÁŘ
Edition
Brno, Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul" 1 pp. 2007
Publisher
Biofyzikální ústav AV CR a Masarykova univerzita-Přírodovědecká fakulta
Other information
Language
English
Type of outcome
Stať ve sborníku
Field of Study
10403 Physical chemistry
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
Organization unit
Faculty of Science
Keywords in English
MD; PAIN; protein; dynamics;
Tags
International impact
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.
In Czech
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.
Links
| GD204/03/H016, research and development project |
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| MSM0021622413, plan (intention) |
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