The Challenge
Bridging Protein–Nanoparticle Interactions for Biomedical Applications
Biomedical nanotechnology applications—from immunoassays to drug delivery and bioimaging—critically depend on understanding how proteins adsorb onto nanoparticle surfaces. Yet the proteome contains over 620,000 protein species, with only ~60,000 having crystal structures available. Traditional all-atom molecular dynamics simulations are computationally prohibitive for high-throughput prescreening across this vast chemical space.
A fast, accessible tool was needed to predict optimal protein orientations and adsorption energies on nanoparticles, enabling researchers and biomedical engineers to rationally design immunoassays, biosensors, and targeted drug delivery systems without requiring deep computational expertise or expensive supercomputing resources.
Our Approach
A rapid multiscale workflow from protein structure to adsorption heatmap
Upload protein structure and define pH conditions
Users provide a PDB file for any protein of interest (up to 2000 residues) and specify the pH environment. The tool automatically handles pH-dependent protonation states of amino acid side chains for realistic electrochemical representation.
Coarse-grain to UnitedAtom representation
Apply the UnitedAtom multiscale model, collapsing the full-atom protein into a coarse-grained representation with one bead per amino acid. This dramatic reduction in degrees of freedom accelerates computation while retaining essential biochemical features.
Configure nanoparticle properties
Define nanoparticle characteristics including material (Ag, Au, Fe₃O₄, PEG, SiO₂, TiO₂), radius, surface potential, and crystallographic plane (hkl). Ionic strength and temperature can be adjusted to match experimental conditions.
Calculate adsorption energy heatmap
Systematically sample protein orientations across the nanoparticle surface and compute adsorption energy for each configuration. Generate a comprehensive energy landscape heatmap identifying preferred binding orientations and relative stability.
Interpret results and export data
Identify the lowest-energy binding mode, examine pH and material dependencies, and download results for integration with downstream applications—from immunoassay design to structure-based drug delivery optimization.