HCOVDOCK help

Help for using HCOVDOCK server

1. How to provide input for docked molecules

The HCOVDOCK server is for predicting the complex structure between a protein and a covalent through a incremental construction sampleing method and a covalent bond-based score function. Users need to provide inputs for the protein and the small molecule to be docked. The HCOVDOCK server can accept input for proteins and peptides:

Upload your pdb file in PDB format.

2. How to add information automatically

The HCOVDOCK supports reading activation residues from receptor's pdb file:

REMARK 800 ACTIVE RESIDUE : A:CYS25

and the HCOVDOCK also supports reading number of virtual atoms and reaction type:

REMARK 801 DUMPY ATOM ONE                  : 30
REMARK 801 DUMPY ATOM TWO                  : 29
REMARK 802 REACTION TYPE                   : Nucleophilic Substitution

3.How to add the virtual atoms

The HCOVDOCK performs covalent docking to predict the binding complexes between a protein and a covalent lignad, in which the virtual atom can be added using other third-party software, such as UCSF chimera.

4. How to obtain your HCOVDOCK 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.
The individual ligand models of the top 20 predictions that were docked to the receptor.
The compressed packages for the top 10 binding models, the top 50 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 ngl software. 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.

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.