Principles of Flexible Protein-Protein Docking

By Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson. 2008

212 citations recorded by the source corpus.

Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein–protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre‐generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small‐scale movements of the backbone and side‐chains are modeled and the binding orientation is improved by rigid‐body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem. Proteins 2008. Published Wiley‐Liss, Inc.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds (2016, unknown): “Thus, it is desirable to develop computational docking methods that, starting from the coordinates of two unbound component molecules defined as receptor and ligand, respectively, are capable of providing a model of acceptable accuracy for the bound receptor-ligand complex [1, 2, 3, 4].”
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 (2017, background): “Molecular docking is a widely-used tool in computer-aided drug design to model the three-dimensional (3D) structure of protein–ligand complexes, study their interactions and predict their binding affinities [1].”
Modeling complexes of modeled proteins (2017, background): “8 Whereas the ultra-low resolution docking may be applicable to cases with large inaccuracies,9 the problem is explicitly addressed by docking methods that allow structure flexibility.”