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

By Yumeng Yan, Di Zhang, Pei-Zhang Zhou, Botong Li, Shengyou Huang. Nucleic Acids Res., 2017

1,262 citations recorded by the source corpus.

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/.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eabb423611534b5fc15c556181bf421b49c63cee

How researchers see this paper

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

In Computational Theory and Mathematics

1. Sheng Wang
2. Huanyu Tao
3. Yumeng Yan
4. Jiahua He
5. Shengua Huang
6. Jianzhu Ma
7. Jian Peng
8. Jiahua Rao

In Molecular Biology

1. Sheng Wang
2. Jinbo Xu
3. Jianzhu Ma
4. Huanyu Tao
5. Yumeng Yan
6. Jiahua He
7. Shengua Huang
8. Yuedong Yang

Citations in the corpus

• HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry (2018, background): “To make protein–protein docking user-friendly, a number of protein–protein docking servers such as ClusPro (4), HADDOCK (5), RosettaDock server (6), GRAMMX (7), 3D-Garden (8), HEX server (9), SwarmDock (10), ZDOCK server (11), PatchDock (12), ATTRACT (13), pyDockSAXS (14), InterEvDock (15) and HDOCK”
• AlphaFold2-aware protein-DNA binding site prediction using graph transformer (2022, background): “promoter prediction) [5], and protein-DNA docking [6] have been widely studied, accurately identifying amino acids involved in protein-DNA interactions solely based on proteins is also an important topic in bioinformatics, which helps to improve molecular docking [7, 8], understand disease mechanism”
• HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, methodology): “Moreover, a hybrid strategy by combining template-based modeling and template-free docking was proposed in HDOCK (19).”
• InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs (2018, methodology): “A hybrid approach combining template-based and templatefree docking was recently proposed in the HDOCK server (18).”
• The HDOCK server for integrated protein–protein docking (2020, methodology): “As shown in our previous study, the scoring functions for protein – protein interactions and protein – RNA interactions are not trans-ferable 37 , although those for protein – RNA interactions and protein – DNA interactions are 27 .”
• Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (2022, methodology): “Next, we use HDOCK [Yan et al., 2017] to dock the antibody template to the target antigen to produce the antibody-antigen complex.”