Performance and its limits in rigid body protein-protein docking

By Israel T. Desta, Kathryn A. Porter, Bing Xia, Dima Kozakov, Sandor Vajda. Structure, 2020

603 citations recorded by the source corpus.

SUMMARY The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions of complex conformations and thus revolutionized protein-protein docking. FFT based methods are now widely available and have been used in hundreds of thousands of docking calculations. Although the methods perform “soft” docking, which allows for some overlap of component proteins, the rigid body assumption clearly introduces limitations on accuracy and reliability. In addition, the method can work only with energy expressions represented by sums of correlation functions. In this paper we use a well-established protein-protein docking benchmark set to evaluate the results of these limitations by focusing on the performance of the docking server ClusPro, which implements one of the best rigid body methods. Furthermore, we explore the theoretical limits of accuracy when using established energy terms for scoring, provide comparison to flexible docking algorithms, and review the historical performance of servers in the CAPRI docking experiment.

Subfields: Biotechnology

View Paper: https://www.semanticscholar.org/paper/9788d39857daacaef4c4bf6a5fec834fc8a16886

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Citations in the corpus

Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (2021, methodology): “We compare our EQUIDOCK method with popular state-of-the-art docking software 2 CLUSPRO (PIPER) (Desta et al., 2020; Kozakov et al., 2017),ATTRACT (Schindler et al.”