Welcome toCGeNArateWeb

Thank you for visiting our website!!

We present CGeNArateWeb, an intuitive environment for simulation of both unconstrained and constrained DNA, such as circular DNA and protein-DNA simulations. The simulations are obtained using CGeNArate, a new model for molecular dynamics simulations for B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution. The method is sequence-dependent and reproduces very well not only local, but also global physical properties of DNA, 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 proteins 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), principal 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).

The source code for the CGeNArate method useful to perform simulations of naked DNA longer than those accessible from this web server is freely available here: CGeNArate method.