How NovaMechanics built an accessible web tool for predicting protein adsorption onto nanoparticles using UnitedAtom coarse-grained modeling — enabling rapid prescreening of biomedical nanotechnology applications without specialized computational expertise. 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. - 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. - 8+ Nanoparticle material types supported - ~60s Computational time for typical protein (1331 residues) - 2000 Maximum residues per protein supported - ~60s Fast Computation: Processing time for 1331 amino acid protein - Heatmap Energy Landscape: Adsorption energy across all protein orientations - 8+ Material Coverage: Ag, Au, Fe₃O₄, PEG, SiO₂, TiO₂ (anatase, rutile) - IgG Case Study Validated: Immunoassay antibody adsorption on Ag NPs - pH-Aware Protonation States: Electrochemically realistic protein representation - Free Web Access: Freely available on Enalos Cloud Platform
