@article {547, title = {CABS-dock standalone: a toolbox for flexible protein-peptide docking}, journal = {Bioinformatics}, volume = {btz185}, year = {2019}, month = {03}, abstract = {CABS-dock standalone is a multiplatform Python package for protein-peptide docking with backbone flexibility. The main feature of the CABS-dock method is its ability to simulate significant backbone flexibility of the entire protein-peptide system in a reasonable computational time. In the default mode, the package runs a simulation of fully flexible peptide searching for a binding site on the surface of a flexible protein receptor. The flexibility level of the molecules may be defined by the user. Furthermore, the CABS-dock standalone application provides users with full control over the docking simulation from the initial setup to the analysis of results. The standalone version is an upgrade of the original web server implementation {\textendash} it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results.CABS-dock standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python and Fortran. The CABS-dock standalone source code, wiki with documentation and examples of use, and installation instructions for Linux, macOS, and Windows are available in the CABS-dock standalone repository at https://bitbucket.org/lcbio/cabsdock}, doi = {10.1093/bioinformatics/btz185}, url = {https://dx.doi.org/10.1093/bioinformatics/btz185}, author = {Maciej Ciemny and Tymoteusz Oleniecki and Aleksander Kuriata and Mateusz Kurcinski and Aleksandra E. Badaczewska-Dawid and Andrzej Koli{\'n}ski and Sebastian Kmiecik} } @article {527, title = {CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures}, journal = {Nucleic Acids Research, gky356}, year = {2018}, abstract = {Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2}, author = {Aleksander Kuriata and Aleksandra Maria Gierut and Tymoteusz Oleniecki and Maciej Ciemny and Andrzej Koli{\'n}ski and Mateusz Kurcinski and Sebastian Kmiecik} } @article {534, title = {CABS-flex standalone: a simulation environment for fast modeling of protein flexibility}, journal = {Bioinformatics}, year = {2018}, pages = {bty685}, abstract = {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}, doi = {10.1093/bioinformatics/bty685}, url = {http://dx.doi.org/10.1093/bioinformatics/bty685}, author = {Mateusz Kurcinski and Tymoteusz Oleniecki and Maciej Ciemny and Aleksander Kuriata and Andrzej Koli{\'n}ski and Sebastian Kmiecik} }