Help for using HDOCK server

1. How to provide input for docked molecules

The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy. Therefore, the user needs to provide input for the two molecule to be docked. The HDOCK server can accept four types of input for molecules:

Only ONE type of input is needed for each molecule.

If more than one types of input are provided, the first will be used. For the "PDB ID:ChainID" input, the user can provide one singel chain ID or multiple chain IDs. For example, "1CGI:E" stands for the chain E of the pdb file of 1CGI; "1AHW:AB" stands for the chains A and B of the pdb file of 1AHW. If only the sequence is provided, the server will automatically constuct a model structure from a homologous template in the Protein Data Bank using a in-house modeling pipeline of HH Suite , Clustaw2, and MODELLER. Currently, the squequence input is only supported for proteins. For DNA/RNA, users need to submit their own structures for docking. In addition, users are also recommended to submit their own pdb file if the protein contains multiple chains, as the pipeline is currently designed to model single-chain proteins.

2.How to specify the binding site [optional]

The HDOCK performs global docking to predict the binding complexes between two molecules. There, no information about the binding site is necessary for the docking job. Howere, the server also gives users the option to specify the binding site residues if such information is available, such that the predicted models will have a higher accuracy. Two types of binding site information can be provided., Lab of Biophysics and Bioinformatics