Detecting interaction sites by docking arbitrary proteins

alex4200 commented 5 years ago

Aspect	Detail
Summary	Web Server to detect and visualize interaction site at protein surface
Usecase Group	Molecular Level
Expert	Guillaume Launay
Scientific User	Structural biologist and Biochemist
Deadline
Target audience	Number of concurrent users unclear.
Target interface	Web Application
HPC Requirements	A Linux cluster running SLURM.
Dependencies	Uses data from rcsb.org
Nominal runtime	3-4 minutes

List of features

Detect protein-protein interaction site at protein surface.
Analyze protein structure, using PDB files as input.
Easy and interactive visualization of the predicted interaction sites.
Amino-acids are assigned individual scores.
The user can visualize the structure of the protein, where amino acids are colored according to their scores.
Submitted proteins can be manipulated either via their structure or their amino acid sequence.
When analyzed protein are multimeric, the user can select different combinations of chains to potentially detect different interaction sites.
Data are displayed in a rich data table.
Results can be dowloaded in tabulated or PDB format.
The service can export data to the Endscript web server to carry additional computations that are complementary to our application.
When in a hurry, the user can be informed by email of the availability of the results.
Session can be restored in the user browser session to later visualized the results.

Link to Application: HERE Link to Tutorial: HERE Link to RCBS: https://www.rcsb.org/

A detailed tutorial is available.

A web browser

Depending on the workload on the back-end infrastructure, results should be obtained in 3-4 minutes.

alex4200 commented 4 years ago

@glaunay Some issues found:

I have selected a pdb file and created some tabs where I removed some of the protein chains, and then clicked on 'Go'. However, even after like 30 minutes the run indication was still 0%.
The email box does not seem to work on chrome (unable to enter characters)
Link to tutorial on the main page would be nice to have.

alex4200 commented 4 years ago

Use case in production, as well as documentation, closing ticket