BilboMD

An advanced Small Angle X-Ray Scattering (SAXS) modelling pipeline.

Description

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.

Pipelines

There are several different SAXS modeling pipelines available.

📊 Interactive pipeline diagrams for each workflow are rendered in the live app — see the Deployment instances below (e.g. Hyperion).

BilboMD Classic w/PDB inputs

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.

BilboMD Classic w/CRD inputs

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.

BilboMD Auto

This pipeline is designed to take Alphafold models and a Per residue Alignment Error (PAE) matrix in combination with your experimental SAXS data.

BilboMD AF

This pipeline is designed to run Alphafold2 on your provided protein sequence and then run the Auto pipeline above.

Test Coverage

Current test coverage across BilboMD apps:

App	Statements	Branches	Functions	Lines
Backend	87.05%	80.65%	86.84%	87.38%
UI	69.82%	61.26%	69.11%	71.07%
Worker	77.76%	64.25%	67.40%	77.55%
Scoper	95.11%	82.14%	88.00%	95.11%

Coverage is automatically updated on each push to main.

Deployment

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.

1. Hyperion https://bilbomd.bl1231.als.lbl.gov

   • Classic w/PDB
   • Classic w/CRD
   • Auto
   • Multi
   • SANS
   • Scoper

2. NERSC https://bilbomd-nersc.bl1231.als.lbl.gov

   • Classic w/PDB
   • Classic w/CRD
   • Auto
   • AF