The HDOCK server (http://hdock.phys.hust.edu.cn/) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information incorporation and job management for robust and fast protein-protein docking. With input information for receptor and ligand molecules (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which experimental information about the protein-protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein-RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two molecules and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min.
Abstract Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applicat...
Abstract Although AlphaFold2 (AF2) and RoseTTAFold (RF) have transformed structural biology by enabling high-accuracy protein structure modeling, they are unable to model covale...
We present a novel protein-ligand docking method that accurately accounts for both ligand and receptor flexibility by iteratively combining rigid receptor docking (Glide) with p...
Molecular docking is an established in silico structure-based method widely used in drug discovery. Docking enables the identification of novel compounds of therapeutic interest...
Modern day drug discovery is extremely expensive and time consuming. Although computational approaches help accelerate and decrease the cost of drug discovery, existing computat...
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