BRIDGE

:bridge_at_night: Biomolecular Reaction and Interaction Dynamics Global Environment

What is BRIDGE ?

BRIDGE developed on the Galaxy platform makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor.

Availability

• BRIDGE tools and source code :books: :wrench:
  • First developed at the Scientific Computing Research Unit, the source code is developed and managed in collaboration with the Galaxy computational chemistry team and is available here.
• BRIDGE tools live on Galaxy :rocket::star:
  • In collaboration with Björn Grüning and the Galaxy computational chemistry team, these tools are available on Galaxy Europe under the Chemical Toolbox section.
  • :computer: Import the example history which contains output from a short molecular dynamics simulation of a fungal hydrolase (7CEL) and then analyse the trajectory using a bio3d inspired workflow (includes PCA, RMSD and RMSF analysis).
• BRIDGE in a 'box' :package:
  • Docker ready to pull (docker pull scientificomputing/bridge; docker run -d -p 8080:80 --rm scientificomputing/bridge , then browse to localhost:8080). See here for more details on starting up a Docker.
  • A Docker file ready to build, see this repository.