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

BilboMD is a web-accessible platform that facilitates integrative modeling of flexible macromolecules using experimental small-angle X-ray and neutron scattering data. BilboMD combines a browser-based interface with high-performance back-end services hosted locally at the SIBYLS beamline and at the National Energy Research Scientific Computing Center (NERSC). BilboMD guides users through a workflow that includes preparing compatible input files, conformational sampling through molecular dynamics (MD) simulations, small-angle X-ray scattering (SAXS) fitting with FoXS, and establishing multi-state models with MultiFoXS. Input assistants (Inp Jiffy and PAE Jiffy) streamline the process of defining rigid and flexible regions for conformational sampling, including automatic inference from AlphaFold PAE matrices. All analyses are containerized to ensure reproducibility, with job metadata and provenance stored in a central database. By leveraging GPU-enabled MD engines, such as OpenMM (on NERSC resources), BilboMD significantly accelerates conformational sampling and expands the set of models used for SAXS fitting. The platform reduces technical barriers for non-specialists while providing API access for advanced users to automate and integrate with custom workflows. Thus, BilboMD democratizes ensemble-based SAXS modeling, accelerates high-throughput SAXS/small-angle neutron scattering analysis, and lays the groundwork for future integration of AI-driven structure prediction with experimental scattering data. It is freely available without a login requirement at https://bilbomd.bl1231.als.lbl.gov.