Details

Autor(en) / Beteiligte

• Desta, Israel T.
• Porter, Kathryn A.
• Xia, Bing
• Kozakov, Dima
• Vajda, Sandor

Titel

Performance and Its Limits in Rigid Body Protein-Protein Docking

Ist Teil von

• Structure (London), 2020-09, Vol.28 (9), p.1071-1081.e3

Ort / Verlag

Elsevier Ltd

Erscheinungsjahr

2020

Link zum Volltext

Quelle

Free E-Journal (出版社公開部分のみ）

Beschreibungen/Notizen

• 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 with flexible docking algorithms, and review the historical performance of servers in the CAPRI docking experiment. [Display omitted] •Protein-protein docking by fast Fourier transform (FFT) samples billions of conformations•FFT-based methods need rigid body approximation and scoring by correlation functions•Rigid methods yield more good models in the top 5 predictions than flexible docking•Flexible methods yield higher accuracy models for some targets Rigid body docking methods, represented here by the ClusPro server, provide acceptable or better models for more complexes than flexible docking methods, but the latter can yield higher accuracy for some targets. In spite of its shortcomings, ClusPro has over 15,000 registered users, and in 2019 performed 98,300 docking calculations.