HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Abstract

Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein–protein and protein–DNA benchmarks and performed better than template-based modeling on the three protein–RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/.

Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology

“…context of an empirical energy function to construct the final predictions. With respect to scoring optimization of the different weighting factors to balance different energetic contributions to the scoring function, as done by other PPI docking methods, [10][11][12][13][14][15][16][17][18][19][20] is anticipated to improve the identified solutions.…”

“…A variety of protein-docking algorithms have been developed and evaluated during last two decades. [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] Some of these algorithms perform global searches to solve the posing problem and usually utilize fast Fourier transforms (FFT) to expedite the scoring of those generated protein poses. 9 Examples include ZDOCK, 10 FTDock, 11 PIPER,12 and GRAMM, 13 among others.…”

Human serum and milk albumins are metal‐dependent DNases

“…NTS binding site is composed of three N-terminal amino acid residues Asp-Ala-His and prefers metal ions capable of square-planar complex formation, e.g. Cu 21 and Ni 21 (32,38). Currently crystal structure of DAHK peptide in complex with Cu 21 as a model of NTS binding site and crystal structure of HSA with Zn 21 bound to MBS binding site are available (31,33).…”

Computational identification of self-inhibitory peptides from white spot syndrome virus envelope protein VP28

“…Using 3D structure of VP28 [PDB:2ed6] as a target for the peptide 3D structure, peptide-protein docking was done by HDOCK server (http://hdock.phys.hust.edu.cn/), which is based on a hybrid algorithm of template-based modeling and ab initio free docking (Yan et al, 2017). The peptide 3D structure was modeled using the PEP-FOLD program, and the best 3D model for the peptide was selected for docking (http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/) (Shen et al, 2014).…”