CABS-flex 2.0

CABS-flex is an efficient procedure for the simulation of structure flexibility of folded globular proteins.

CABS-flex is a protein simulation tool that implements the CABS simulation engine (which is the coarse-grained protein model reviewed here) for fast simulations of proteins flexibility. CABS-flex is presently available as the webserver 2.0 and as the standalone package. In comparison to the web-server, the standalone package offers many more functionalities that enable guiding the modeling process and combinations with other tools.

The development, functionalities, and applications of the CABS-flex method have been described so far in the following papers:

7Protocols for fast simulations of protein structure flexibility using CABS-flex and SURPASS

Methods in Molecular Biology, submitted, 2019
Badaczewska-Dawid Aleksandra, Kolinski Andrzej, Kmiecik Sebastian

6CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures

Nucleic Acids Res, 46: W338-W343, 2018
Kuriata Aleksander, Gierut A. M., Oleniecki T., Ciemny Maciej, Kolinski A., Kurciński Mateusz Kmiecik Sebastian

5CABS-flex standalone: a simulation environment for fast modeling of protein flexibility

Bioinformatics, 4: 694–695, 2018
Kurciński Mateusz , Oleniecki T., Ciemny MaciejKuriata Aleksander, Kolinski A., Kmiecik Sebastian

4AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

Nucleic Acids Research, 43: W306-W313, 2015
Zambrano Rafael, Jamroz Michal, Szczasiuk Agata, Pujols Jordi, Kmiecik Sebastian, Ventura Salvador

3CABS-flex predictions of protein flexibility compared with NMR ensembles

Bioinformatics, 30: 2150-2154, 2014
Jamroz Michal, Kolinski Andrzej, Kmiecik Sebastian

2CABS-flex: server for fast simulation of protein structure fluctuations

Nucleic Acids Research, 41: W427-W431, 2013
Jamroz Michal, Kolinski Andrzej, Kmiecik Sebastian

1. 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: 119-125, 2013
Jamroz Michal, Orozco Modesto, Kolinski Andrzej, Kmiecik Sebastian