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

Summary: CABS‐flex standalone is a Python package for fast simulations of protein structure flexibility. The package combines simulations of protein dynamics using CABS coarse‐grained protein model with the reconstruction of selected models to all‐atom representation and analysis of modeling results. CABS‐flex standalone is designed to allow for command‐line access to the CABS computations and complete control over simulation process. CABS‐flex standalone is equipped with features such as: modeling of multimeric and large‐size protein systems, contact map visualizations, analysis of similarities to the reference structure and configurable modeling protocol. For instance, the user may modify the simulation parameters, distance restraints, structural clustering scheme or all‐atom reconstruction parameters. With these features CABS‐flex standalone can be easily incorporated into other methodologies of structural biology. Availability and implementation: CABS‐flex standalone is distributed under the MIT license, which is free for academic and non‐profit users. It is implemented in Python. CABS‐flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS‐flex standalone repository at https://bitbucket.org/lcbio/cabsflex.

[1]  M. Feig,et al.  Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields. , 2017, Journal of chemical theory and computation.

[2]  A. Kolinski.  Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.

[3]  Rafael Zambrano,et al.  AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures , 2015, Nucleic Acids Res..

[4]  Andrzej Kolinski,et al.  CABS-flex: server for fast simulation of protein structure fluctuations , 2013, Nucleic Acids Res..

[5]  Modesto Orozco,et al.  Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. , 2013, Journal of chemical theory and computation.

[6]  Sergey Lyskov,et al.  PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta , 2010, Bioinform..

[7]  A. Kolinski,et al.  Coarse-Grained Protein Models and Their Applications. , 2016, Chemical reviews.

[8]  Mateusz Kurcinski,et al.  CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures , 2018, Nucleic Acids Res..

[9]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[10]  A. Kolinski,et al.  Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction , 2016, Scientific Reports.

[11]  Mateusz Kurcinski,et al.  CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site , 2015, Nucleic Acids Res..

[12]  Adam K. Sieradzan,et al.  A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions , 2014, Journal of Molecular Modeling.

[13]  Andrzej Kolinski,et al.  CABS-flex predictions of protein flexibility compared with NMR ensembles , 2014, Bioinform..

[14]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.