MCDNA-lite is the webserver associated to the publication A multimodal coarse-grain model of DNA flexibility mappable to the atomistic level (Walther et al.). MCDNA-lite takes advantage of the extended next-to-nearest neighbor (enNN) model to provide the user a limited number of alternative equilibrium B-DNA conformations according to the tetrameric states of the underlying sequence. The structures are then subject to atomistic detail reconstitution. For more details on the enNN-model and its capabilities to reproduce atomistic molecular dynamics (MD) simulations and experimental structures the user is referred to the publication (see above).
As input the user only needs to specify a DNA sequence and optionally his email address in case he wants to receive an email with the link to the output. The calculation time of a DNA sequence of typical length of 20nt lies in the second regime. The resulting conformations (up to 20) can be viewed interactively in the ‘Output’ ia ‘View structure in 3D’ where each row of the table (sorted by decreasing probability) corresponds to one alternative DNA structure. The inter base pair parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are shown for each structure in a pop-up table by clicking on ‘View parameters’. The user can also load each structure into NAFlex (a tool for setting up and analyzing MD simulations, doi: 10.1093/nar/gkt378) where a set of setup workflows can be applied (with different force fields and different MD packages –AMBER, GROMACS, NAMD-). The relative probability of the resulting conformations - the probability of a structure is calculated as the multiplication of the individual probability of each chosen tetrameric state and normalized so that the sum of all probabilities equals to one – are shown in the last column.
At both ends of the table three buttons allow executions using the ensemble of structures: (1) the ensemble of structures can also serve as input for flexibility analysis via ‘Analyze Ensemble (NAFlex), including helical parameters, principal component analysis, or NMR observations’, (2) the button 'View all structures' allows the visualization of a selection of the ensemble of conformations in the same window and (3) via the 'Download all results' button the user can download all generated results: DNA conformations in pdb format, the inter base pair parameter file of each structure and a file with the probability of each configuration.
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
Jürgen Walther , Pablo D Dans, Alexandra Balaceanu, Adam Hospital, Genís Bayarri, Modesto Orozco.
Nucleic Acids Research, Volume 48, Issue 5, 18 March 2020, Page e29,