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.
"Select a type" is not needed for structure input, as the HDOCK server is able to guess a general type of protein or RNA/DNA according to the input structure. However, for sequence input, users are strongly recommended to select a molecular type, because the HDOCK server may not be able to correctly guess the molecular type based on the sequence only. Here are the definitions of different molecular types:
Protein Standard protein molecule
RNA General single-chain RNA molecule
DNA General single-chain DNA molecule
DNA/duplex Right Handed B-DNA duplex molecule
RNA/duplex Right Handed A-RNA duplex molecule
DNA/strand Single-stranded helical DNA molecule
RNA/strand Single-stranded helical RNA molecule
2. RNA/DNA 3D structure modeling
HDOCK server now accepts
sequence inputs for RNA/DNA. Only a single sequence is needed, which can
contain the sequence only like this
or both the sequence and its secondary structure like this
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
NOTE For each restraint, the first field is for receptor, the second field is for ligand, and the third field is for the constrained distance. The residue representation must be in num:chainID or num1-num2:chainID format, where the residue number and chain ID refer to the input structure if the input is a structure, or the modeled structure if the input is a sequence.
CAUTION For the 3D structure modeled by the server, the chain ID is set to “A” for single-chain molecule, and “A” and “B” for a DNA/RNA duplex structure. The numbering of residues is consistent with that in the input sequence.
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.