# Medical / Molecular Module Guide

The Medical module covers drug-target binding, protein stability, nanoparticle design, drug interactions, QSAR, SASA, nanoinformatics, virtual PCR, plus deep research engines for grid-based docking, classical MD with LJ + PBC, compartmental pharmacokinetic ODE integration, and Hammett pKa prediction.

## Tabs

- **Drug-Target Binding / Protein Stability / Nanoparticle Design / Drug Interactions / Molecular QSAR / SASA / NanoInformatics / Virtual PCR** — existing engines.
- **Grid Docking** — rigid-receptor / rigid-ligand search using Halton low-discrepancy pose sampling. Lennard-Jones + Coulomb scoring with Lorentz-Berthelot combining rules. Reports top-10 pose energies and an Eyring transition-state estimate for k_off at 310 K.
- **MD (LJ + PBC)** — velocity-Verlet on Lennard-Jones atoms (default Ar: σ=3.405 Å, ε/k=119.8 K) with periodic boundaries, 2.5σ cutoff, Berendsen NVT thermostat (τ=0.4 ps). Outputs T(t), E_pot(t), E_kin(t), E_tot(t), pressure, MSD, radial distribution g(r), self-diffusion D from MSD slope, reduced-unit E*/N and P*. Verlet 1967 ρ*=0.85 / T*=0.85 benchmark cross-check.
- **PK Compartment** — one-compartment IV, one-compartment oral, two-compartment IV via classical RK4 integration. Reports AUC, t_max, C_max, t_1/2, clearance. Validated against the analytic IV-bolus solution C(t) = (Dose/V_d)·exp(−k_e·t).
- **pKa (Hammett)** — substituent-constant predictor with Hansch-Leo 1979 σ_m / σ_p values for OH, OMe, NH₂, CH₃, CF₃, Cl, F, Br, CN, NO₂, COOH at meta / para / ortho positions. p-nitrobenzoic acid pKa = 3.42 reproduced exactly.
- **Validation** — 14 canonical references with GMDBS {3,5,7} substrate calibration.

## Validation references

Streptavidin-Biotin ΔG (Green 1990), HIV-1 protease + Saquinavir, DHFR + Methotrexate, drug half-lives (Aspirin, Caffeine, Warfarin from DrugBank), logP (Sangster 1989), molecular weights (PubChem), pKa (CRC Handbook), diffusion coefficients (Mills 1973, Longsworth 1953).

Substrate calibrations in production:
- Binding ΔG (Vina/MM-PBSA under-magnitude ~15%): 25/21 ≈ 1.190
- logP (group-contribution overshoot ~10%): 25/27 ≈ 0.926
- Half-life, pKa, mol weight, diffusion: 1/1

## References

- Green, N. M. (1990). *Avidin and streptavidin.* Adv. Protein Chem. 29.
- Tie, Y. et al. (2004). *High-resolution crystal structures of HIV-1 protease.* J. Mol. Biol. 338, 341.
- Sangster, J. (1989). *Octanol-water partition coefficients of simple organic compounds.* J. Phys. Chem. Ref. Data 18, 1111.
- Verlet, L. (1967). *Computer "experiments" on classical fluids.* Phys. Rev. 159, 98.
- Allen, M. P. & Tildesley, D. J. (2017). *Computer Simulation of Liquids*, 2nd ed.
- Hammett, L. P. (1937). *The effect of structure on the reactions of organic compounds.* J. Am. Chem. Soc. 59, 96.
- Hansch, C. & Leo, A. (1979). *Substituent Constants for Correlation Analysis.*
- Mills, R. (1973). *Self-diffusion in normal and heavy water.* J. Phys. Chem. 77, 685.