CABS-flex is an efficient procedure for the simulation of structure flexibility of folded globular proteins. It is based on the CABS model, the well-established coarse-grained protein modeling tool. The CABS may generate consistent protein dynamics at highly reduced (3 orders of magnitude) cost, although with some decrease of resolution. The CABS-flex server follows the work of Jamroz, Orozco, Kolinski and Kmiecik [ ref 1], 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. This observation have been confirmed in further extensive validation tests [ read NAR paper].
The only data required as an input is a protein structure in PDB format (or a protein PDB code). The input structure is used as a starting point for the CABS simulation of near-native dynamics. The resulting trajectory is automatically analyzed and processed to provide the useful description of protein dynamics in the following outputs:
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-means method) and subsequent multi-step reconstruction and optimization procedures (the procedures were extensively tested in previous protein dynamics and structure prediction studies).
The CABS-flex server pipeline is presented below (different kinds of output data are marked in blue):
The CABS-flex server employs the following tools:
Note that by using the predicted models from the CABS-flex server you agree with all the licenses of external tools listed above.
Comparison of CABS Dynamics with Molecular Dynamics on 393 protein data set.
Current server load | 0.2/12 |
Uptime | 15w 5d 9h 2m 27s |
Projects, finished | 1699 |
Projects, pending | 0 |
Projects, total | 1714 |
Modelled aminoacids, total | 257799 |
© Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw 2013