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.
This repository is the code for the website part of the CGeNArate docker web services.
David Farré-Gil, Genís Bayarri, Adam Hospital.
This website has been developed by the MMB group at the IRB Barcelona.
© 2025 Institute for Research in Biomedicine
Licensed under the Apache License 2.0.