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

@article{Yan2017HDOCKAW,
  title={HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy},
  author={Yumeng Yan and Di Zhang and Pei-Zhang Zhou and Bo-tong Li and Shengyou Huang},
  journal={Nucleic Acids Research},
  year={2017},
  volume={45},
  pages={W365 - W373}
}
Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. [...] Key Result The docking process is fast and consumes about 10-20 min for a docking run.Expand
Modeling Protein-Protein or Protein-DNA/RNA Complexes Using the HDOCK Webserver.
TLDR
This chapter first briefly introduces the HDOCK server, a protein-protein/nucleic acid docking web server, and gives a step-by-step description of docking bovine chymotrypsinogen A against its inhibitor (PDB ID: 1CGI). Expand
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TLDR
A homology model-based ensemble docking approach to explicitly consider the protein flexibility in protein-RNA docking through an ensemble of multiple protein structures, which is referred to as MPRDock and will have a general application in molecular docking for other interactions. Expand
HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
TLDR
HNADOCK, a user-friendly web server for nucleic acid (NA)–nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, is presented, where both sequence and structure inputs are accepted for RNAs, while onlyructure inputs are supported for DNAs. Expand
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A robust RNA–protein fragment pair-based method, termed RnaX, to predict RNA-binding sites and reengineer the interface at the sequence-specificity level by mimicking those conformational changes that occur on protein and RNA mutagenesis. Expand
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TLDR
This paper compares the difference between the free docking and the template-based algorithm and shows the complementarity of these two methods, and shows that P3DOCK is better than those two non-hybrid docking algorithms. Expand
Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46
TLDR
The results validated the HDOCK server as an efficient automated docking protocol for nonexpert users as well as challenges and opportunities of automated docking. Expand
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs
TLDR
The InterEvDock2 pipeline was benchmarked on 812 complexes for which unbound homology models of the two partners and co-evolutionary information are available in the PPI4DOCK database and identified a correct model among the top 10 consensus in 29% of cases and at least one correct interface residue among 10 predicted in 91% of these cases. Expand
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry
TLDR
HSYMDOCK is presented, a web server of the authors' hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry and obtained a significantly better performance than other similar docking algorithms. Expand
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
TLDR
The HawkDock server is a powerful tool to predict the binding structures and identify the key residues of PPIs and could achieve a better performance than ZDOCK 3.0 in the benchmark testing. Expand
GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
TLDR
GalaxyHeteromer is a freely available automatic web server that predicts protein heterodimer complex structures from two subunit protein sequences or structures, and employs one of the best ab initio docking methods whenheterodimer templates are unavailable. Expand
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