What Method to Use for Protein-Protein Docking?

By Kathryn A. Porter, Israel T. Desta, Dima Kozakov, Sandor Vajda. 2019

88 citations recorded by the source corpus.

A number of well-established servers perform “free” docking of proteins of known structures. In contrast, template-based docking can start from sequences if structures are available for complexes that are homologous to the target. Based on the results of the CAPRI-CASP structure prediction experiments, template-based methods yield more accurate predictions if good templates can be found, but generally fail without such templates. However, free global docking, or focused docking around even poor quality template-based models, can still generate acceptable docked structures in these cases. Based on the analysis of a benchmark set, free docking of heterodimers yields acceptable or better predictions in the top 10 models for around 40% of structures. However, it is likely that a combination of template-based and free docking methods can perform better for targets that have template structures available. Another way of improving the reliability of predictions is adding experimental information as restraints, an option built into several docking servers.

Subfields: Biotechnology, Ecology, Radiology, Nuclear Medicine and Imaging

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The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Radiology, Nuclear Medicine and Imaging

1. Bing Xia
2. Kathryn A. Porter
3. Israel T. Desta
4. Dima Kozakov
5. Sandor Vajda
6. D. Ritchie

Citations in the corpus

• Improved prediction of protein-protein interactions using AlphaFold2 (2021, methodology): “Shape complementary approaches rely on protein structures or models of the monomers 8,9 , while template-based docking needs suitable templates.”
• Performance and its limits in rigid body protein-protein docking (2020, methodology): “In many cases such structures have homologous templates available in the Protein Data Bank (PDB), and the problems can be solved by homology modeling without the need for any docking (Porter et al., 2019a).”
• The HDOCK server for integrated protein–protein docking (2020, background): “Since its release in 2017, the HDOCK server has been well received by the research community 28 – 35 and completed >30,000 jobs from around the world.”
• Application of docking methodologies to modeled proteins (2020, methodology): “27,28 Since the comparative docking methods are based on proteins alignments, as opposed to the free docking which is based on surface complementarity, they are generally less sensitive to the conformational changes upon binding.”