HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry

By Yumeng Yan, Huanyu Tao, Shengyou Huang. 2018

50 citations recorded by the source corpus.

Abstract A major subclass of protein–protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling of the symmetric protein complexes is important for understanding the molecular mechanism of related biological processes. Although several symmetric docking algorithms have been developed for Cn symmetry, few docking servers have been proposed for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK server was extensively evaluated on three benchmarks of symmetric protein complexes, including the 20 CASP11–CAPRI30 homo-oligomer targets, the symmetric docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained a significantly better performance than other similar docking algorithms. The server supports both sequence and structure inputs for the monomer/subunit. Users have an option to provide the symmetry type of the complex, or the server can predict the symmetry type automatically. The docking process is fast and on average consumes 10∼20 min for a docking job. The HSYMDOCK web server is available at http://huanglab.phys.hust.edu.cn/hsymdock/.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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. Shourya S. Roy Burman
2. Huanyu Tao
3. Shengua Huang
4. Jiahua He
5. Jeffrey J. Gray
6. Remy A. Yovanno
7. Yumeng Yan

In Materials Chemistry

1. Jeffrey J. Gray
2. Shourya S. Roy Burman
3. Remy A. Yovanno
4. Yumeng Yan
5. Huanyu Tao
6. Shengua Huang
7. Jiahua He

In Molecular Biology

1. Shourya S. Roy Burman
2. Remy A. Yovanno
3. Huanyu Tao
4. Shengua Huang
5. Jiahua He
6. Jeffrey J. Gray
7. Yumeng Yan
8. Brian G. Pierce

Citations in the corpus

• Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment (2019, neutral): “Increasing use was also made of docking algorithms that incorporate symmetry operations (eg, HSYMDOCK-lite 72 ), or of algorithms that handle multiple chains (eg, Multi-LZerD 73 ) or better account for conformational flexibility.”
• Flexible backbone assembly and refinement of symmetrical homomeric complexes (2018, methodology): “Recently, four leading symmetric docking methods were evaluated on a benchmark of 251 complexes, 180 of which were homodimers (Yan et al., 2018).”
• The HDOCK server for integrated protein–protein docking (2020, methodology): “For Dn symmetric multimer docking, it can be realized by a Cn plus C2 docking 68 .”