CABS-flex is an efficient modeling procedure for fast simulations of protein structure flexibility [1]. It is based on the CABS model, a well-established coarse-grained protein modeling tool – CABS design and applications have been recently reviewed in [2]. 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 [3] – follows the work of Jamroz et al. [4], 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 [5]. CABS-flex method is also used as a part of the AGGRESCAN3D method for the prediction of protein aggregation propensity [6] (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).