Protein Pathfinder

Protein Interaction Pathfinder turns two gene names into a fully evidenced, visually explorable interaction pathway — combining STRING network data, structural biology, and expression validation in one research tool. WHETHER YOU'RE MAPPING A SIGNALING CASCADE, checking whether two proteins can plausibly interact in a specific cell line, or just want to see a protein's real electrostatic surface, this app builds the evidence trail for you instead of leaving you to stitch together five different databases by hand. KEY FEATURES Pathway Discovery • Enter any two human gene symbols and find the shortest interaction path between them • Choose your evidence type: Functional, Physical, or directional Regulatory (v12 or the v12.5 preview with activation/inhibition signs) • See the full STRING evidence breakdown for every edge — experimental, curated database, text mining, co-expression, neighborhood, gene fusion, and co-occurrence scores • Jump straight to the live STRING network graph for any pair Independent Dual-Panel 3D Structures • View both proteins' real PDB structures side by side, each with its own camera • Rotate and zoom each protein independently with a single touch — no more fighting over a shared view • Overlay phosphorylation sites directly on the 3D surface Electrostatic Surface Visualization • Color each protein's surface by charge — red for negative, blue for positive — computed from real CHARMM27 force-field partial charges across nearly every atom, not just a handful of charged residues • Fine-tune the approximation yourself: histidine protonation state, contrast, Debye screening length, and visual intensity are all adjustable sliders • A fast, on-device approximation built for exploration — not a substitute for a full Poisson-Boltzmann calculation, and the app is upfront about that distinction Cell-Type Expression Validation • Check whether both proteins in an interaction are actually expressed together in a specific cancer cell line (HeLa, MCF-7, MDA-MB-468, A549, and more) or a primary tissue cell type • Pulls real single-cell and cell-line RNA expression data from the Human Protein Atlas • Flags subcellular co-localization so you can see whether two co-expressed proteins are even in the same compartment PhosphoSite Validation • Cross-reference kinase-substrate relationships against OmniPath and SIGNOR • See which phosphorylation sites on a substrate are actually documented for a given kinase Chemical Interaction Context • Surface known small-molecule / chemical interaction data from STITCH for either protein in your pathway Built-In Guide • A full in-app user guide explains every screen, every data source, and every scoring system — no external documentation hunting required WHY IT'S DIFFERENT Most interaction-mapping tools stop at "these two proteins are connected." Protein Interaction Pathfinder asks the next three questions automatically: What kind of evidence supports that connection? Would these two proteins ever actually meet inside a real cell? And what does their physical interface actually look like? Answering all three normally means juggling STRING, the PDB, and the Human Protein Atlas in separate browser tabs — this app does it in one pass, on your phone. DATA SOURCES All data is pulled live from established, citable public resources: STRING (protein interaction evidence), RCSB PDB (3D structures), the Human Protein Atlas (expression data), OmniPath and SIGNOR (phosphorylation evidence), and STITCH (chemical interactions). Nothing is scraped or pre-baked — every query reflects the current state of these databases. WHO IT'S FOR Built for structural and cancer biologists, phosphoproteomics researchers, bioinformatics students, and anyone who needs a fast, evidence-backed answer to "how — and where — do these two proteins actually interact?" Authors: Heebok Lee, Ph.D. and Gihoon Lee, Ph.D. — offered to the research community as a courtesy.