BilboMD: a web-accessible SAXS and AlphaFold-guided modeling pipeline.

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Macromolecular modeling is crucial for understanding biological function.
• Experimental scattering data (SAXS/SANS) provides low-resolution structural information.
• Integrating experimental data with computational modeling remains challenging.

Purpose of the Study:

• To introduce BilboMD, a web-accessible platform for integrative modeling of flexible macromolecules.
• To streamline the process of conformational sampling and scattering data fitting.
• To reduce technical barriers for researchers in macromolecular modeling.

Main Methods:

• Utilizes a browser-based interface with high-performance computing resources.
• Incorporates molecular dynamics (MD) simulations for conformational sampling.
• Employs FoXS and MultiFoXS for small-angle X-ray scattering (SAXS) data fitting.
• Containerization ensures reproducibility of analyses.
• Input assistants streamline preparation of simulation parameters.

Main Results:

• BilboMD facilitates integrative modeling using SAXS and small-angle neutron scattering (SANS) data.
• The platform accelerates conformational sampling through GPU-enabled MD engines.
• It enables the establishment of multi-state models for flexible macromolecules.
• Input assistants simplify defining regions for conformational sampling, including AlphaFold PAE inference.

Conclusions:

• BilboMD democratizes ensemble-based SAXS modeling.
• The platform accelerates high-throughput SAXS/SANS analysis.
• BilboMD integrates experimental data with computational modeling, paving the way for AI-driven structure prediction.