CABS-flex is an efficient modeling procedure for fast simulations of protein structure flexibility . It is based on the CABS model, a well-established coarse-grained protein modeling tool – CABS design and applications have been recently reviewed in . The CABS model may generate protein dynamics at highly reduced (3 orders of magnitude) computational cost, although with some decrease in resolution. The CABS-flex server – version 1.0 has been introduced in 2013  – follows the work of Jamroz et al. , where the authors demonstrated, that the consensus view of protein near-native dynamics obtained from 10-nanosecond MD simulations (all-atom, explicit water, for all protein metafolds using the four most popular force-fields), is consistent with the CABS dynamics. It has been also demonstrated that fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles . CABS-flex method is also used as a part of the AGGRESCAN3D method for the prediction of protein aggregation propensity  (AGGRESCAN3D employs CABS-flex to take into account the influence of the dynamic protein structure fluctuations on the aggregation propensity). Moreover, CABS-flex methodology is a component of the CABS-dock method for protein-peptide docking [7-9] , which allows for significant flexibility of the peptide and the protein receptor during explicit simulation of peptide binding.
The only data required as input is a protein structure in the PDB format (or a protein PDB code). The input structure is used as a starting point for the CABS simulation. The resulting trajectory is automatically analyzed and processed to provide the useful description of protein dynamics (see Figure 1).
An important attribute of protein models generated by the CABS is that their spatial resolution (in C-alpha chain format) allows for reconstruction of all-atom representation of physically realistic models. The output set of all-atom models is generated through trajectory clustering (by k-medoids method) and subsequent multi-step reconstruction and optimization procedures (using Modeller package