P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking

Bioinformatics. 2020 Jan 1;36(1):96-103. doi: 10.1093/bioinformatics/btz478.

Abstract

Motivation: The main function of protein-RNA interaction is to regulate the expression of genes. Therefore, studying protein-RNA interactions is of great significance. The information of three-dimensional (3D) structures reveals that atomic interactions are particularly important. The calculation method for modeling a 3D structure of a complex mainly includes two strategies: free docking and template-based docking. These two methods are complementary in protein-protein docking. Therefore, integrating these two methods may improve the prediction accuracy.

Results: In this article, we compare the difference between the free docking and the template-based algorithm. Then we show the complementarity of these two methods. Based on the analysis of the calculation results, the transition point is confirmed and used to integrate two docking algorithms to develop P3DOCK. P3DOCK holds the advantages of both algorithms. The results of the three docking benchmarks show that P3DOCK is better than those two non-hybrid docking algorithms. The success rate of P3DOCK is also higher (3-20%) than state-of-the-art hybrid and non-hybrid methods. Finally, the hierarchical clustering algorithm is utilized to cluster the P3DOCK's decoys. The clustering algorithm improves the success rate of P3DOCK. For ease of use, we provide a P3DOCK webserver, which can be accessed at www.rnabinding.com/P3DOCK/P3DOCK.html. An integrated protein-RNA docking benchmark can be downloaded from http://rnabinding.com/P3DOCK/benchmark.html.

Availability and implementation: www.rnabinding.com/P3DOCK/P3DOCK.html.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Benchmarking
  • Internet*
  • Molecular Docking Simulation* / methods
  • Molecular Docking Simulation* / standards
  • Proteins* / metabolism
  • RNA* / metabolism
  • Software

Substances

  • Proteins
  • RNA