BSM-Arc

BSM-Arc archives and distributes raw in silico structural biology data, including computationally modeled 3D structures and molecular dynamics trajectories, to support research in protein folding, drug design, and biomolecular interactions.

Key Features:

• Raw data archival: Archives computationally modeled 3D structures and molecular dynamics (MD) trajectories as raw in silico outputs.
• Format flexibility: Accepts depositor-uploaded raw files without requiring prior conversion to a specific format.
• Submission annotation: Supports depositor-provided annotations including detailed textual explanations and illustrative figures.
• Interactive visualization (Molmil): Provides the Molmil WebGL-based molecular viewer to recreate interactive 3D scenes from publications.
• Provenance and publication linkage: Requires ORCID-based login authentication and association of each submission with a peer-reviewed publication prior to public release.
• Data dissemination: Makes archived datasets available for third-party access to enable validation, reuse, and comparative analyses.

Scientific Applications:

• Protein folding: Provides modeled structures and MD trajectories for studying protein folding mechanisms.
• Drug design: Supplies computational models and trajectories used in structure-based drug design and ligand interaction analysis.
• Biomolecular interactions: Enables analysis of macromolecular complexes and biomolecular interaction interfaces from modeled structures and dynamics.
• Validation and reproducibility: Facilitates validation studies and reproducibility by providing access to raw computational datasets and annotations.
• Figure recreation and validation: Allows recreation of 3D scenes depicted in scientific articles to support figure validation and methodological transparency.

Methodology:

BSM-Arc ingests depositor-uploaded raw computational outputs (modeled 3D structures and molecular dynamics trajectories), stores them with depositor-provided annotations and illustrative figures, exposes interactive visualization via the Molmil WebGL viewer, and enforces ORCID authentication with linkage to a peer-reviewed publication before public release.