BRIDGE
| Public server: | BRIDGE Server |
|---|---|
| Container: | BRIDGE in Docker |
| Scope: | Domain specific |
| Summary: | Prepare, simulate and analyse and visualise molecular simulations, especially molecular dynamics and free energies. |
Comments
- BRIDGE (Biomolecular Reaction and Interaction Dynamics Global Environment) is a Computational Chemistry flavour of Galaxy - a webserver for preparing, simulating and analysing and visualising molecular simulations, especially molecular dynamics and free energies. Software such as NAMD, GROMACS and CHARMM can be used to define and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor.
User Support
- Tutorial: Free energy calculations for drug discovery
- Tutorial: High Throughput Molecular Dynamics and Analysis (and more GTN computational chemistry training)
- Gitter Support Channel
Quotas
- Storage and computational quotas.
Citations
- Senapathi, T., Barnett, C. B., & Naidoo, K. J. (2020). BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations. Bio-Protocol, 10(17), e3731–e3731. doi: 10.21769/BioProtoc.3731
- Senapathi, T., Bray, S., Barnett, C. B., Grüning, B., & Naidoo, K. J. (2019). Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE). Bioinformatics. doi: 10.1093/bioinformatics/btz107
- BRIDGE tagged publications in the Galaxy Publication library
Sponsors
- Developed at the Scientific Computing Research Unit of the University of Cape Town.
- This BRIDGE server is hosted as part of the Galaxy CompChem ZA project on the ILIFU resources.