The HDOCK server is to predict the binding complexes between two molecules like proteins and nucleic acids by using a hybrid docking strategy. Therefore, users need 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 one will be used. For the "PDB ID:ChainID" input, the user can provide one single 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 a 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. In addition, users are also recommended to submit their own pdb file if the protein contains multiple chains, as our pipeline is currently designed to model single-chain proteins.
>example GGAGCGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAGUCCCGUCCGUUCCGCCAor both the sequence and its secondary structure like this
>example GGAGCGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAGUCCCGUCCGUUCCGCCA (((((((..((((.........))))((((.(((((...))))))))).(((((.......))))))))))))....HDOCK will then build its 3D structure based on the single sequence, or model a 3D duplex structure by construting a complementary Watson-Crick paired second strand.
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
0.0000E+00 1.4612E+07 3.0685E+03 1.0000E-03 1.4743E+07 4.8653E+03 2.0000E-03 1.4827E+07 7.3394E+03 3.0000E-03 1.4685E+07 1.0573E+04 4.0000E-03 1.4674E+07 1.3206E+04 5.0000E-03 1.4659E+07 1.5831E+04 6.0000E-03 1.4729E+07 1.5466E+04 7.0000E-03 1.4707E+07 1.7649E+04 8.0000E-03 1.4594E+07 2.3642E+04 9.0000E-03 1.4787E+07 2.8835E+04With the SAXS experimental curve, the final solutions will be ranked according to their CHI values that measure the goodness of the predicted binding modes fitting to the SAXS experimental data.