Work

Principles of flexible protein–protein docking

Year: 2008

Type: review

Abstract: 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.

Source: Proteins Structure Function and Bioinformatics

DOI: 10.1002/prot.22170

Authors: Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson

Institutions: Tel Aviv University, National Cancer Institute, Center for Cancer Research, Science Applications International Corporation (United States)

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Tel Aviv University, National Institutes of Health, National Cancer Institute, National Institute of Allergy and Infectious Diseases

Awards: G1356092923, DCTD Computer Support, G1799052500, Broad-Spectrum Antagonist of Superantigen Toxins