CABS-flex 2.0


server for fast modeling of protein structure flexibility. CABS-flex 2.0 implements an efficient simulation engine that allows for modeling of large-scale conformational transitions of protein systems.


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CABS-flex 2.0 applications include modeling flexibility of globular proteins, proteins with disordered regions of significant length, loop flexibility and dynamics of selected protein fragments (where the allowed degree of protein flexibility is defined by user with distance restraints).

Near-native dynamics of globular proteins

In simulations of flexibility of globular proteins, the CABS-flex was shown to be a computationally efficient alternative to all-atom molecular dynamics – a classical simulation approach.

Large-scale rearrangements of disordered protein fragments

CABS-flex 2.0 enables to assign a full flexibility to selected protein fragments. This option has been used in protein-peptide docking to protein receptor with flexible regions of significant length.

Influence of protein flexibility on protein aggregation properties

CABS-flex method can be used as a component of methods for structure-based prediction of protein aggregation properties. CABS-flex is presently used as a part of AGGRESCAN3D web server.



How to

Papers describing the CABS-flex server, methodology and its utilization in other modeling pipelines


CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

Kuriata, A.*, Gierut, A. M.*, Oleniecki, T., Ciemny, M. P., Kurcinski, M., Kmiecik, S. (2018). CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic acids research.


CABS-flex: server for fast simulation of protein structure fluctuations (1st server version)

Jamroz, M., Kolinski, A., & Kmiecik, S. (2013). CABS-flex: server for fast simulation of protein structure fluctuations. Nucleic acids research, 41(W1), W427-W431.

CABS-flex predictions of protein flexibility compared with NMR ensembles

Jamroz, M., Kolinski, A., & Kmiecik, S. (2014). CABS-flex predictions of protein flexibility compared with NMR ensembles. Bioinformatics, 30(15), 2150-2154.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field

Jamroz, M., Orozco, M., Kolinski, A., & Kmiecik, S. (2012). Consistent view of protein fluctuations from all-atom molecular dynamics and coarse-grained dynamics with knowledge-based force-field. Journal of chemical theory and computation, 9(1), 119-125.

AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

Zambrano, R., Jamroz, M., Szczasiuk, A., Pujols, J., Kmiecik, S., & Ventura, S. (2015). AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures. Nucleic acids research, 43(W1), W306-W313.



Contact

CABS-flex 2.0 allows to present protein models in a web browse using high-performance 3Dmol graphics library. To facilitate perception and enhance the experience, the surface can be displayed/hidden and the structure can be animated showing rotation about a vertical axis.

Gallery

CABS-flex 2.0 provides also interactive contact maps created using the D3.js library to present an interaction within a pair of residues in each given chain. Maps can be transformed and scaled to facilitate recognition of in smaller areas with the possibility of changing the colour scale.