BSDB

BSDB provides simulation-derived mechanostability data for proteins to characterize their responses to mechanical stretching.

Key Features:

• Structure-based model simulations: Simulations of 17,134 proteins performed within a structure-based model to probe mechanostability under stretching.
• Maximal Force Peaks: Quantitative heights of maximal force peaks observed during stretching experiments.
• Force-Displacement Patterns: Detailed force-displacement patterns that illustrate how proteins deform under applied force.
• Sequencing of Contact-Rupturing Events: Records the sequence in which contacts within a protein structure rupture during stretching.
• Mechanical clamps and motifs summaries: Comprehensive summaries of potential mechanical clamps or motifs responsible for resistance to stretching.

Scientific Applications:

• Structural biology: Interpretation of mechanostability in terms of structural motifs and contact-rupturing sequences.
• Biophysics: Quantitative assessment of mechanical stability using maximal force peaks and force-displacement patterns.
• Protein engineering: Guiding the design of more mechanically stable proteins by identifying mechanical clamps and rupture sequences.
• Experimental design: Informing stretching experiments with simulation-derived force profiles and predicted rupture order.
• Biomaterials science: Supporting selection or design of mechanically robust biomolecules based on simulation-derived metrics.

Methodology:

Simulations of 17,134 proteins were performed using a structure-based model to capture mechanistic responses to stretching.