Skip to content

FpocketWeb is a browser app for identifying pockets on protein surfaces where small-molecule ligands (e.g., drugs) might bind. It runs the fpocket executable entirely in a web browser. The pocket-finding calculations occur on the user’s computer rather than a remote server.

License

durrantlab/fpocketweb

Repository files navigation

FPocketWeb 1.0.0

Introduction

FPocketWeb runs fpocket, a popular program for identifying cavities in protein surfaces, entirely in a web browser. The pocket-hunting calculations occur on the user's own computer rather than a remote server. The FPocketWeb app includes a convenient interface, so users can easily set up their pocket-finding runs and analyze the results. A working version of the app can be accessed free of charge from http://durrantlab.com/fpocketweb.

Compatibility

We have tested FPocketWeb on all major operating systems (Linux, macOS, Windows, Android, iOS) and web browsers (Chrome, Firefox, Safari, Edge).

Description of Use

Input Parameters Tab

The "Input Parameters" tab includes the "Input File" and "Advanced Parameters" subsections. In the "Input File" subsection, users can specify the protein file (PDB format) for pocket hunting. The contents of these files are loaded into the browser's memory, but they are never transmitted/uploaded to any third-party server. Users who wish to simply test FPocketWeb can instead click the "Use Example File" button to load a preprepared structure of H. sapiens heat shock protein 90 (Hsp90, PDB 5J2V). Loaded files are displayed in the "PDB Preview" subsection using a 3Dmol.js molecular viewer.

The "Advanced Parameters" subsection allows users to specify the same parameters available through the fpocket command-line executable, so they can fine-tune the underlying pocket-finding method. FPocketWeb initially hides these parameters because most users will prefer to use the default values. Once ready, users can click the "Start FPocketWeb" button to initiate the FPocketWeb run.

Output Tab

FPocketWeb displays the "Output" tab once the calculations are complete, which includes the "Visualization" and "Detected Pockets" subsections, among others. The "Visualization" subsection displays the specified protein and detected cavities. Initially, only the pocket with the highest fpocket score is displayed.

The "Detected Pockets" subsection contains a table with the detailed output for each detected pocket, one pocket per row. Initially, only the score, the druggability score, the number of alpha spheres, and the volume are displayed, but the "Show Details" toggles allow users to display all other fpocket metrics for each detected pocket. Users can also change the color used to visualize each pocket.

The "Output Files" subsection allows users to view the FPocketWeb output PDB file directly. This file includes the original protein structure and all the detected pockets. Users can press the associated "Download" button to save the file to disk.

Finally, the "Run Fpocket from the Command Line" subsection provides a code snippet so users can run fpocket from the command line with the same FPocketWeb parameters used in the browser.

Start Over Tab

The "Start Over" tab displays a simple button that allows the user to restart the FPocketWeb app. A warning message reminds the user that they will lose the results of the current FPocketWeb run unless they have saved their output files.

Running FPocketWeb on Your Own Computer

Most users will wish to simply access the already compiled, publicly available FPocketWeb web app at http://durrantlab.com/fpocketweb. If you wish to instead run FPocketWeb on your own UNIX-like computer (LINUX, macOS, etc.), follow these instructions:

  1. Download the fpocketweb.zip file
  2. Uncompress the file: unzip fpocketweb.zip
  3. Change to the new fpocketweb/ directory: cd fpocketweb
  4. Start a local server. We recommend using Node.js and npm:
    • npm install -g http-server
    • http-server
  5. Access the server from your web browser (e.g., http://localhost:8080/, http://0.0.0.0:8080/, http://127.0.0.1:8080/, etc.)

Running FPocketWeb on other operating systems (e.g., Windows) should be similar.

Notes on User Analytics

In some circumstances, the FPocketWeb web app may report usage statistics to Google Analytics. These reports are useful for securing and justifying funding for the Durrant lab. Usage statistics are only sent if the web-app URL contains the substring "durrantlab," so installing FPocketWeb on your own server should prevent reporting. Even when using the publicly available version of FPocketWeb hosted at http://durrantlab.com/fpocketweb, information about your specific protein is never transmitted to any remote server.

About

FpocketWeb is a browser app for identifying pockets on protein surfaces where small-molecule ligands (e.g., drugs) might bind. It runs the fpocket executable entirely in a web browser. The pocket-finding calculations occur on the user’s computer rather than a remote server.

Resources

License

Stars

Watchers

Forks

Packages

No packages published