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.
195:A, 203-206:A, 108:Bwhich stand for residues 195, 203-206 of chain A, and 108 of chain B. Note that the residues in a line must be separated by comma.
The binding site residues may also be submitted as a file that will look like this
195:A 203-206:A 108:B
195:A 236:B 8, 215-218:A 306:B 6where the distance of residue 195 of chain A on the receptor and residue 236 of chain B on the ligand will be within 8 A; The distance of residues 215-218 of chain A on the receptor and residue 306 of chain B on the ligand will be within 6 A. Likewise, the above distance restraints can also be provided as a file that looks like this
195:A 236:B 8 215-218:A 306:B 6