Help for using HPEPDOCK server

1. How to provide input for docked molecules

The HPEPDOCK server is for predicting the complex structure between a protein and a peptide through a hierarchical flexible peptide docking approach by fast conformational modeling and orientational sampling of peptides. Users need to provide inputs for the protein and the peptide to be docked. The HPEPDOCK server can accept four types of input for proteins and peptides:

• Upload your pdb file in PDB format.
• Provide your structure by PDB ID:ChainID (e.g. 3BFW:A).
• Copy and paste your protein/peptide sequence in FASTA format.
• Upload your protein/peptide sequence file in FASTA format

Only ONE type of input is needed for each molecule.

If more than one type 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, "3BFW:A" stands for the chain A of the pdb file of 3BFW; "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 construct a model structure from a homologous template in the Protein Data Bank using an in-house modeling pipeline of HH Suite , Clustaw2, and MODELLER. As our pipeline is currently designed to model single-chain proteins, if the protein contains multiple chains, users are also recommended to submit their own pdb file.

2.How to specify the binding site [optional]

The HPEPDOCK performs global flexible-peptide docking to predict the binding complexes between a protein and a peptide, in which the binding site information can be extracted from the complex structures in the Protein Data Bank if available. 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 if users provide their protein input as a pdb file or structure, such that the predicted models will have a higher accuracy. Two types of binding site information can be provided.

• Binding site residues on the protein.
The binding site residues provided in the text box must be separated by comma as follows

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

which stand for residues 195, 203-206 of chain A, and 108 of chain B. Please be sure that the "number(s):chain" of provided residues should be consistent with information in the input protein structure or pdb file.
• Binding site reference pdb file.
The binding site may also be defined through a reference pdb file like the native peptide or ligand structure in PDB format around which the peptide will be docked on the protein.

3. How to obtain your HPEPDOCK results.

Once users submit their 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 job is finished.
• 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 when they submit their job.

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

• Receptor PDB file uploaded by users or constructed by the server from the FASTA sequence provided by users.
• The individual peptide models of the top 20 predictions that were docked to the receptor.
• The compressed packages for the top 10 binding models, the top 100 binding models, or all the docking results.

Since the top 10 binding models are normally deemed as the most important models, the result page also 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 peptide binding.

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 docking results should be downloaded as soon as possible once a docking job is done, as the job results will only be stored on our server for two weeks.

© Lab of Biophysics and Molecular Modeling, huanglab@hust.edu.cn