An advanced Small Angle X-Ray Scattering (SAXS) modelling pipeline.
BilboMD is a webapp developed at the SIBYLS beamline. It uses Molecular Dynamics from CHARMM or OpenMM to generate an array of possible molecular models. The ensemble of models is used to calculate theoretical SAXS curves using FoXS, and compared with experimental SAXS data using MultiFoXS to find an ensemble of models that best explains your SAXS data.
There are several different SAXS modeling pipelines available.
This pipeline offers the classic BilboMD from years past where you can upload a custom const.inp file and adjust the rg_min and rg_max values. It takes a user provided PDB file and experimental SAXS data.
This pipeline offers the classic BilboMD from years past where you can upload a custom const.inp file and adjust the rg_min and rg_max values. It takes a user provided CRD and PSF file and experimental SAXS data. The CRD and PSF files can be generated using CHARMM GUI.
This pipeline is designed to take Alphafold models and a Per residue Alignment Error (PAE) matrix in combination with your experimental SAXS data.
This pipeline is designed to run Alphafold2 on your provided protein sequence and then run the Auto pipeline above.
Current test coverage across BilboMD apps:
| App | Statements | Branches | Functions | Lines |
|---|---|---|---|---|
| Backend | 80.00% | 64.15% | 71.73% | 80.50% |
| UI | 65.58% | 55.56% | 62.64% | 67.16% |
| Worker | 82.40% | 71.34% | 83.09% | 82.48% |
| Scoper | N/A | N/A | N/A | N/A |
Coverage is automatically updated on each push to main.
There are 2 instances of BilboMD available. Each deployment has a different selection of pipelines available. This is primarily because of access to high performance NVIDIA GPUs at NERSC which are unavailable at the SIBYLS beamline on Hyperion.
-
Hyperion https://bilbomd.bl1231.als.lbl.gov
- Classic w/PDB
- Classic w/CRD
- Auto
- Multi
- SANS
- Scoper
-
NERSC https://bilbomd-nersc.bl1231.als.lbl.gov
- Classic w/PDB
- Classic w/CRD
- Auto
- AF