How to use IFACE Surface Comparison Online

Use IFACE online to compare two protein structures by molecular-surface geometry and chemistry.

IFACE (Intrinsic Field-Aligned Coupled Embedding) compares two protein molecular surfaces through a shared geometric and physicochemical representation. It combines intrinsic surface structure with mean curvature, electrostatic potential, hydrogen-bonding propensity, and hydrophobicity, producing both a joint distance and an interpretable probabilistic correspondence between surface vertices.

On Neurosnap, users upload a reference protein structure and a query protein structure. The service applies the modified MaSIF preparation described by the IFACE paper to generate each molecular surface and its vertex-level chemical fields, then cleans and samples each mesh to approximately 1,000 vertices before comparison.

How IFACE Surface Comparison Works

Surface preparation starts from each uploaded PDB or mmCIF structure. Neurosnap removes non-protein entities, adds hydrogens with Reduce, constructs a solvent-excluded molecular surface with MSMS, computes electrostatic potential with PDB2PQR and APBS, and assigns MaSIF hydrogen-bonding and Kyte-Doolittle hydrophobicity fields. The documented IFACE preprocessing then cleans and decimates the mesh, transfers continuous properties over local surface neighborhoods, smooths the reduced mesh, and computes mean curvature directly on that mesh.

IFACE computes intrinsic geodesic distances and optimizes a soft coupling between the two prepared surfaces. Results include the aggregate IFACE distance, geometry and chemistry subtotals, individual feature distances, the full coupling matrix, and the two strongest query correspondences for every reference vertex. Distances are most useful comparatively across jobs prepared by this same protocol; a soft correspondence is not proof that individual residues or atoms are functionally equivalent.

What is Neurosnap?

Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.

Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.

Advancing Discovery with IFACE Surface Comparison on Neurosnap

Using IFACE Surface Comparison on Neurosnap could drastically accelerate structure-to-surface generation and joint geometric-chemical comparison in one workflow.

Structure-native input: Researchers provide ordinary PDB or mmCIF protein structures directly.
Documented preparation: Surface generation follows the modified MaSIF feature pipeline and the mesh-sampling procedure described for IFACE.
Unified distance: Shape, curvature, electrostatics, hydrogen bonding, and hydrophobicity contribute to one interpretable score.
Inspectable alignment: The full coupling matrix and top vertex correspondences expose how the distance was formed.

How to Use IFACE Surface Comparison on Neurosnap

To harness the capabilities of IFACE Surface Comparison, researchers can follow this streamlined workflow within Neurosnap:

Access Neurosnap: Start by logging in to the Neurosnap website.
Select Tool: From the list of available tools, choose IFACE Surface Comparison.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the IFACE Surface Comparison job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.

Citations

Please cite the original work when using IFACE Surface Comparison in publications or research outputs.

Swami H, McBride JM, Eckmann JP, Tlusty T. Joint Geometric-Chemical Distance for Protein Surfaces. arXiv:2603.09860. 2026.

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/

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