#Dock it solves protein series#

The CABS (name comes from the names of pseudo-atoms: C-Alpha, C- Beta and the Side-chain) representation of protein backbone is reduced to just two pseudo-atoms per single residue, one representing the center of the alpha-carbon and another one placed at the center of the C-alpha-C-alpha pseudo-bond (Figure 1). 7) is utilized by the CABS-dock method as a simulation engine. 2 THE CABS MODELĬABS-a coarse-grained model of protein structure, interactions, and dynamics (see review by Kmiecik et al. 5, 6, 13- 19 Those are briefly discussed in the “CABS-dock applications” section together with the remaining challenges and potential ways of addressing these issues.

#Dock it solves protein series#

Over the past few years, the CABS-dock applications have been presented in a series of publications. In the “CABS-dock method” section, we describe the current status of the CABS-dock tool, its design and its major features. The most prospective way to achieve this aim is by the skillful application of the available distance restraints, as demonstrated in this article. Our intent was to make the CABS model usable by a wide group of scientists, who could tailor the simulation setup and conditions directly to their needs. On top of the CABS model, the CABS-dock tool has been designed primarily to address the problem of the protein–peptide docking, but also to encapsulate the raw CABS procedures within a user-friendly interface. The CABS model representation, interaction, and sampling schemes are briefly described in the next section. Thanks to the sampling efficiency, the CABS-dock offers a unique opportunity for on-the-fly simulation of the flexibility of peptide and protein receptor molecules during the search for the binding site (other methods rather rely on rigid docking that is sometimes merged with the next step of flexible refinement 4, 9- 12). 8 The natural cost of such a speedup is loss of accuracy, which has been mostly averted thanks to the clever design of the protein representation. It has been estimated that in terms of the computational efficiency the CABS model surpasses Molecular Dynamics speed by about three to four orders of magnitude. 7 It allows for modeling of the long timescale conformational rearrangements of polypeptide chains, like the process of peptide folding and its simultaneous binding to the flexible protein receptor in a single CABS-dock simulation run. It has proven to be an extremely efficient tool in many applications. The central module of the CABS-dock method is its fast simulation engine: the CABS coarse-grained protein model. While the web server is dedicated to quick and easy setup of docking simulations and browsing of modeling results, the standalone version is designed for power users interested in the most advanced feature set. Motivated by a large number of users and their various demands, in 2018 we presented the standalone version 6 (available at ).

CABS-dock is a global docking method that we introduced in 2015 as a web server 5 (available at ). Generally, the template-based docking uses known structures of the receptor–peptide complexes as scaffolds, the local docking is limited to the predefined binding site, while the global docking tools are designed to search for both the binding site and the peptide pose. Protein–peptide docking methods can be divided into three categories 4: template-based docking, local docking, and global docking techniques. In recent years, a variety of computational tools have been developed for docking of peptides to proteins, 4 that is, prediction of the three-dimensional structures of the protein–peptide complexes. Since the experimental characterization can be difficult, or costly and time-consuming, computational methods have become important supporting tools and in many cases an attractive alternative. 1- 3 The vast array of new technologies is being employed to facilitate the discovery of new peptide-based drugs, including those aiming at the structural characterization of peptide interactions with their protein targets. Peptide drug discovery is currently a very active research field with great potential for addressing unmet medical needs.