Molecular dynamics recipes for genome research.
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect.
Cellular and Molecular Biology.
Tommaso
T
Biagini
Biochemistry and Molecular Biology.
Giovanni
G
Chillemi
American Physiological Society.
Gianluigi
G
Mazzoccoli
Cineca Specialistic User Support group.
Alessandro
A
Grottesi
Statistics for Biomedicine.
Caterina
C
Fusilli
Life Sciences, `La Sapienza' University of Rome.
Daniele
D
Capocefalo
Cellular and Molecular Biology.
Stefano
S
Castellana
Bicocca University of Milan.
Angelo Luigi
AL
Vescovi
IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, viale Regina Margherita, Rome, Italy.
Tommaso
T
Mazza
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic / Q000706:statistics & numerical data; D023281:Genomics / Q000706:statistics & numerical data*; D006801:Humans; D056004:Molecular Dynamics Simulation / Q000706:statistics & numerical data*; D020641:Polymorphism, Single Nucleotide; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D012984:Software; D012985:Software Design
D011506:Proteins