CABS-dock standalone: a toolbox for flexible protein–peptide docking

Abstract

Summary 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—it introduces a number of customizable options, provides support for large-sized systems and offers a framework for deeper analysis of docking results. Availability and implementation CABS-dock standalone is distributed under the MIT licence, 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.

Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement

“…The main goal of this work was to deliver an easy to use and efficient protocol for the accurate prediction of peptide ligand binding modes to the GPCR protein family. The protocol employs three state-of-the-art tools for the multiscale modeling of protein-peptide interactions [20][21][22][23]42]. All these tools proved to be very effective for handling modeling tasks for many different systems consisting of cytosolic proteins.…”

“…CABS-dock has been first introduced as a web server [36][37][38] and successfully applied to modeling large-scale conformation changes of protein receptor during peptide binding [39], protein-protein docking [38], peptide docking using sparse information on protein-peptide residue-residue contacts [40] and modeling the cleavage events occurring during proteolytic peptide degradation [41]. Recently, CABS-dock has been made available as a standalone application [20], which contains many features and extensions for advanced users. The repository of the CABS-dock package, which includes tutorials and description of commands, is available at https://bitbucket.org/lcbio/cabsdock/.…”

“…In this work, we used the CABS-dock standalone application [20] with the following input information (the structural data including peptide sequence information and restraint parameters used for CABS-dock input preparation for each of the 7 modeled systems are presented in Supplementary Table S1):…”

“…In this work, we present the modeling protocol dedicated for prediction of GPCRpeptide complexes that combines a coarse-grained CABS-dock global docking tool [20] with PD2 [21] reconstruction of the backbone and C-beta atoms positions and high-resolution…”

Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures

“…Computational, or even experimental, structure characterizations often require reconstruction of missing atoms and/or models refinement to a higher resolution. This is also the case for the CABS-dock method [2,3] a well-established tool for protein-peptide docking.…”