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:

2. How to add information automatically

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

REMARK 800 ACTIVE RESIDUE : A:CYS25

2.How to add the virtual atoms [optional]

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.

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

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.