Help for using HSYMDOCK server

1. How to provide input for the molecule to be docked

The HSYMDOCK server is for predicting the structure of protein complexes with Cn and Dn symmetry through a hybrid docking strategy. Users need to provide the subunit molecule and the symmetry type information as input. The HSYMDOCK server accepts four types of input for the monomers:

• Upload your pdb file in PDB format.
• Provide your structure by PDB ID:ChainID (e.g. 5A6X:A).
• Copy and paste your protein sequence in FASTA format.
• Upload your protein sequence file in FASTA format

Only ONE type of input is needed for the subunit molecule.

If more than one types of input is provided, the first one will be used. For input as "PDB ID:ChainID", users can provide one single chain ID or multiple chain IDs. For example, "5A6X:A" stands for the chain A of the pdb file of 5A6X; "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 build a 3D structure from a homologous template in the Protein Data Bank using our in-house homology modeling pipeline of HH Suite , Clustaw2, and MODELLER. In addition, users are recommended to submit their own pdb file or structure if the subunit protein contains multiple chains, as our pipeline is currently designed to model single-chain proteins.

Users have an option to provide the symmetry type. However, it the symmetry type is not provided, the server will predict the symmetry type automatically by searching for the homologous complexes in the PDB.

2.How to specify the binding site [optional]

The HSYMDOCK performs a global docking to predict the symmetrical complexes from a subunit molecule. Therefore, no information about the binding site is required for the docking job. However, the server also gives users an option to specify the binding site residues if such information is available, such that the predicted models will have a higher accuracy. The binding interface/site information can be provided as follows.

• Binding site resdiues on the subunit molecule.
The binding site residues can be provided like this in the text box

	195:A, 203-206:A, 108:B

which stand for residues 195, 203-206 of chain A, and 108 of chain B. The residues in a line must be separated by comma. Please be sure that the "number(s):chain" of provided residues should be consistent with information in the input protein structure or pdb file.

3. How to obtain your HSYMDOCK results.

Once users submit your job, they will be redirected to a status web page showing the status of the job. The status page is automatically refreshed every 10 seconds until the job is finished. Users have three ways to obtain their docking results.

• Keep the status page open until it shows the docking results when the docking results is ready.
• Bookmark the status page and come back later to check the docking results.
• Wait for the email notification if users provide a valid email address at the time of job submission.

After the job is done, users will then be redirected to the result papge, from which they can download the following files

• The individual complex models of the top 20 predictions that are docked from the subunit molecule.
• The compressed packages for the top 10 predictions, the top 100 predictions, or all the docking results.

As the top 10 binding models are normally deemed as the most important models, the result page provides an interactive view of the top 10 models using the Jmol software, where the receptor and the peptide are colored differently. Users can choose to view any of the top 10 models or all together by different representations and styles.

The page also gives a summary of the rankings and docking scores for the top 10 binding models. However, it should be noted that the docking scores here do not reflect the real binding affinities, but a relative ranking of the binding between subunits. For Cn symmetry the score reflects the interactions between all neighboring subunit proteins. For docking with Dn symmetry, the score represents a summation of the interactions from all the binding interfaces between subunits.

In addition, if only a sequence is provided as the input for the protein, the page will also show the information about the modeled protein structure by homology modeling, including the used template, model quality, sequence alignment and sequence identity between the template and the input sequence.

NOTE: It is recommended that users download their docking results as soon as possible after the job is done, as the job results will only be stored on our server for two weeks.