Pro Tier Module
PROTAC / Dual-PROTAC Ternary Audit
An exact three-body ternary-complex equilibrium solver for PROTAC targeted protein degradation, and a mechanistic AUDIT for dual PROTACs.
This tool runs inside GDBS Pro. What it computes and the authorities it applies are below.
What it is
An exact three-body ternary-complex equilibrium solver for PROTAC targeted protein degradation, and a mechanistic AUDIT for dual PROTACs. From the two binary dissociation constants (target-PROTAC, PROTAC-E3) and the cooperativity factor alpha it computes the ternary-complex concentration, the hook-effect dose-response, and the optimal PROTAC dose (Douglass et al. JACS 2013; Han JBC 2020). For a dual PROTAC (two targets sharing one E3 ligase) it solves the coupled competition equilibrium and answers the field audit questions numerically: a valency-benefit ratio (does the dual beat the best single-axis bivalent at matched ligase + dose?), a per-axis degradation-flux split, and an effectively-single-axis flag. Honest scope: alpha and the Kd values are measured INPUTS (SPR/ITC), not predicted from structure; ternary occupancy is the mechanistic driver of degradation, not a DC50/Dmax prediction; no docking, no MD, no clinical claim. Deterministic, in-browser, no API/key/network/AI - GeoNum conditioning trust read from the real kernel drift compartment (canonical shade ladder), with the mass-balance residual reported separately as solver accuracy.
Honest scope
Deterministic and citation-backed: every figure is exact arithmetic or a cited rule. Any year- or jurisdiction-indexed value is a confirmable input, never an eternal hardcode. This is a computation tool, not professional (legal, tax, medical, or financial) advice - confirm against the controlling authority for your context.
Authorities cited
- Douglass, E.F. Jr.; Miller, C.J.; Sparer, G.; Shapiro, H.; Spiegel, D.A. "A Comprehensive Mathematical Model for Three-Body Binding Equilibria." J. Am. Chem. Soc. 2013, 135(16), 6092-6099. doi:10.1021/ja311795d. The exact three-body (ternary) binding-equilibrium framework and cooperativity treatment this solver implements.
- Han, B. "A suite of mathematical solutions to describe ternary complex formation and their application to targeted protein degradation by heterobifunctional ligands." J. Biol. Chem. 2020, 295(45), 15280-15291. doi:10.1074/jbc.RA120.014715. PROTAC-specific closed-form ternary solutions, cooperativity alpha, and the hook effect.
- Perelson, A.S.; DeLisi, C. "Receptor clustering on a cell surface. I. Theory of receptor cross-linking by ligands bearing two chemically identical functional groups." Math. Biosci. 1980, 48, 71-110. The multivalent cross-linking equilibrium lineage the PROTAC ternary solutions rederive (noted in the 2021 JBC comment on Han 2020).
- Gadd, M.S.; Testa, A.; Lucas, X.; et al. "Structural basis of PROTAC cooperative recognition for selective protein degradation." Nat. Chem. Biol. 2017, 13, 514-521. doi:10.1038/nchembio.2329. Structural/biophysical basis of the cooperativity alpha used here as a measured input (definition alpha = Kd_binary/Kd_ternary).
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Run it on your own data
Open it inside GDBS to save runs to Sandbox, attach results to a Worklog case, or share through a Gate client portal - all in the browser, nothing uploaded to anyone’s cloud.