// profile
Computational pharmacologist working at the intersection of genetic algorithms and statistical mechanics. Main author of FlexAIDΔS, a genetic-algorithm docking engine that computes the full ΔG = ΔH − TΔS — the conformational entropy term included, recovering the correct binding mode where enthalpy-only scoring fails. Every result is reproducible by construction and shipped under Apache 2.0. Anti-prohibitionist; harm reduction as applied thermodynamics. Montréal.
// research interests
molecular docking
statistical mechanics of binding
conformational entropy
free-energy scoring
genetic-algorithm optimization
Shannon entropy
drug repurposing / off-targets
open-source scientific software
harm reduction
// education
Ph.D. — Pharmacology (in progress)
Université de Montréal · Najmanovich Research Group (NRGlab)
Thesis: entropy-driven molecular docking — FlexAIDΔS and the full ΔG = ΔH − TΔS score.
present
M.Sc. — Biochemistry
Université de Sherbrooke · NRGlab (origin lab)
Docking methods, contact-based scoring, and the first NRGsuite / FlexAID toolchain.
conferred
B.Sc. — Structural Bioinformatics
Université Laval
Foundations in structural biology, protein modelling and computational methods.
conferred
// research & engineering experience
Doctoral researcher
Fall 2017 — present
Najmanovich Research Group (NRGlab) · Université de Montréal
- ›Main author of FlexAIDΔS: a C++26 genetic-algorithm docking engine with a full statistical-mechanics score (ΔG = ΔH − TΔS), torsional ENCoM entropy, Voronoi contact function and dead-end-elimination torsion pruning.
- ›96.4% correct binding-mode recovery on Astex Diverse 85 — without crystal coordinates.
- ›Built Python bindings and the NRGsuite PyMOL plugin; zero-copy GPU/OpenMP batch scoring for high-throughput screens.
Lead programmer
2014 — present
Najmanovich Research Group (NRGlab)
- ›Principal software architect for the lab — own the NRG docking toolchain end to end across its Sherbrooke and Montréal eras.
Founder · maintainer
2023 — present
Le Bonhomme Pharma · github.com/LeBonhommePharma
- ›Open-science pharmacology lab shipping reproducible Apache-2.0 tooling from Little Burgundy, Montréal.
- ›Ported the FlexAIDΔS entropy kernel to two new domains — Shannon (LLM entropy-collapse) and ClusterFuck (HRV biofeedback).
Graduate researcher
earlier
NRGlab · Université de Sherbrooke
- ›Co-developed NRGsuite and applied FlexAID to large-scale off-target detection for drug repurposing and side-effect prediction.
// software & open source
FlexAIDΔS
C++26 · Python · PyMOL
Apache 2.0
Entropy-driven molecular docking engine. GA conformational search, Voronoi contact function, torsional ENCoM entropy, DEE torsion pruning, zero-copy GPU/OpenMP batch scoring. The full ΔG = ΔH − TΔS.
Shannon
C++20 · Python
Apache 2.0
Entropy-collapse detector for frontier LLM agents — zero-shot evaluation-awareness and strategic-deception monitoring via the same H = −Σ pᵢ log₂ pᵢ kernel that powers binding and HRV.
ClusterFuck
Swift · HealthKit · CareKit
Apache 2.0
Multi-platform Apple biofeedback (Watch · iPhone · TV · Vision Pro). Real-time HRV entropy → Shannon Collapse Index during guided chair yoga; shared kernel with FlexAIDΔS.
NRGsuite
Python · PyMOL
open source
PyMOL plugin packaging the NRGlab docking toolchain for real-time interactive docking with FlexAID.
PoseBust
C++26
open source
PoseBusters-compatible geometric validation — physical-plausibility checks (bond geometry, clashes, planarity) for docked ligand poses.
// benchmarks & technical results
96.4%
Astex Diverse 85 · top pose
85%
cross-dock · RMSD < 2Å
94%
Shannon · collapse sens.
| Benchmark |
Metric |
Result |
| Astex Diverse 85 |
correct binding mode (top pose) |
96.4% |
| Astex Diverse 85 |
cross-dock, RMSD < 2Å |
85% |
| Shannon |
entropy-collapse sensitivity |
94% |
// publications
preprints & in preparation
-
P1
Morency L-P, Najmanovich RJ. FlexAIDΔS: entropy-driven molecular docking with a full ΔG = ΔH − TΔS statistical-mechanics score. Preprint / in preparation. 2026
-
P2
Morency L-P. Shannon: entropy-collapse detection for frontier LLM agents via the FlexAIDΔS configurational-entropy kernel. Preprint. 2026
peer-reviewed
-
01
Morency L-P, Gaudreault F, Najmanovich RJ. Applications of the NRGsuite and the molecular docking software FlexAID in computational drug discovery and design. Methods in Molecular Biology 1762, 367–388. Humana Press. 2018
-
02
Chartier M, Morency L-P, Zylber MI, Najmanovich RJ. Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. BMC Pharmacology and Toxicology 18, 18. 2017
-
03
Gaudreault F, Morency L-P, Najmanovich RJ. NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID. Bioinformatics 31(23), 3856–3858. 2015
invited talks & conference keynotes
-
K1
Morency L-P, Najmanovich RJ. Modelling conformational entropy in molecular docking — beyond the enthalpy-only score. PROTEO Annual Symposium, Québec (invited). 2019
// talks & teaching
workshops
Hands-on docking with NRGsuite and FlexAID in PyMOL — graduate computational-biology methods.
invited
Entropy is not optional: why enthalpy-only docking gets the right answer for the wrong reason.
teaching
Teaching assistant, biochemistry & structural bioinformatics — Université de Sherbrooke.
// technical skills
Languages
C++26
C++20
Python
Swift
CMake
Bash
Scientific
Molecular docking
Statistical mechanics
Free-energy scoring
Normal-mode / ENCoM
Shannon entropy
HRV signal processing
Tooling
PyMOL
OpenMP
CUDA / GPU
Git
HealthKit
CareKit
Practice
Reproducible builds
Open-source maintenance
Benchmark design
Apache 2.0 / MIT
// awards & funding
Médaille du Lieutenant-Gouverneur du Québec (bronze)
Cabinet du Lieutenant-gouverneur du Québec — academic & civic merit.
—
Doctoral research fellowship
Fonds de recherche du Québec — Nature et technologies (FRQ-NT).
PhD
Open-source contribution recognition
GitHub Arctic Code Vault Contributor; multi-year maintainer across the NRGlab / Le Bonhomme Pharma stack.
—
// writing & advocacy
Book in progress — housing, organized crime, and harm reduction in Montréal. The same physics that lowers a binding free-energy barrier lowers the social barrier to care: systems seek lower free energy; the job is to lower it.
Drug of the Day — a rotating, rigorous harm-reduction pharmacology brief published at thebonhomme.com. Mechanism over moralising.
Le Bonhomme Pharma · Little Burgundy · Montréal · Québec
ΔG = ΔH − TΔS