@article {554, title = {Computational reconstruction of atomistic protein structures from coarse-grained models}, journal = {Computational and Structural Biotechnology Journal}, volume = {18}, year = {2020}, pages = {162-176}, abstract = {Three-dimensional protein structures, whether determined experimentally or theoretically, are often too low resolution. In this mini-review, we outline the computational methods for protein structure reconstruction from incomplete coarse-grained to all atomistic models. Typical reconstruction schemes can be divided into four major steps. Usually, the first step is reconstruction of the protein backbone chain starting from the C-alpha trace. This is followed by side-chains rebuilding based on protein backbone geometry. Subsequently, hydrogen atoms can be reconstructed. Finally, the resulting all-atom models may require structure optimization. Many methods are available to perform each of these tasks. We discuss the available tools and their potential applications in integrative modeling pipelines that can transfer coarse-grained information from computational predictions, or experiment, to all atomistic structures.}, keywords = {coarse-grained modeling, protein modeling, protein reconstruction, structure prediction, structure refinement}, issn = {2001-0370}, doi = {https://doi.org/10.1016/j.csbj.2019.12.007}, url = {http://www.sciencedirect.com/science/article/pii/S2001037019305537}, author = {Aleksandra E. Badaczewska-Dawid and Andrzej Koli{\'n}ski and Sebastian Kmiecik} } @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} }