Welcome to MC DNA
Thank you for visiting our website!!
The name of the webserver was inspired by the sampling method used to simulate DNA structures. MCDNA uses Monte Carlo sampling to obtain a set of representative DNA conformations at base pair step level accuracy. MCDNA provides an intuitive environment where in addition to simulations of unconstrained DNA MCDNA can simulate DNA in a constrained environment such as circular DNA and protein-DNA simulations while its performance exceeds common molecular dynamics simulations by several orders of magnitude.
Apart from the sequence it is possible to choose the resolution of the simulated DNA ('Coarse Grain' or 'Atomistic') and the type of operation to execute ('Create Structure' and 'Create Trajectory') which makes the webserver a flexible tool that can be tailored to the user's needs. Additionally, in the case of 'circular DNA' the amount of initial over- or undertwisting can be specified. In 'protein-DNA' the user can manually indicate the protein(s) to be superimposed onto the DNA at a given position in the sequence.
The graphical output of the simulations is complemented with a flexibility analysis done by Curves+ (backbone torsions, BI/BII, alpha/gamma, sugar puckering, grooves, axis base pair and inter base pair parameters), princial component analysis, contact matrix, bending and energy penalty calculations as well as individual analysis depending on the chosen simulation type (see more details in Help).
MCDNA is integrated in the Virtual Research Environment of the MuG project (https://www.multiscalegenomics.eu).
There is a complete Help section accessible through the main menu on the top of the page. But if you want to see a short introduction to this website, you can click the button below:
Jürgen Walther, Genís Bayarri, Adam Hospital, Felipe Cano, Víctor López-Ferrando, J. Lluís Gelpí, Pablo D. Dans and Modesto Orozco.
Molecular Modeling and Bioinformatics Group