Louis-Philippe (LP) Morency
Computational pharmacologist · docking-engine author · open-science
PhD candidate · Najmanovich Research Group · Université de Montréal
scholar.google.com · L-P Morency
ORCID 0009-0001-0218-4750
// 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 dockingstatistical mechanics of bindingconformational entropyenthalpy-entropy compensationfree-energy scoringgenetic-algorithm optimizationShannon entropydrug repurposing / off-targetsopen-source scientific softwareharm reduction
// education
Ph.D. − Pharmacology (in progress)
Université de Montréal · Najmanovich Research Group
Thesis: entropy-driven molecular docking − FlexAIDΔS and the full ΔG = ΔH − TΔS score.
present
M.Sc. − Biochemistry
Université de Sherbrooke · Najmanovich Research Group (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 researcherFall 2017 − present
Najmanovich Research Group · 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.
- Running the Astex Diverse 85 self- and cross-docking campaign without crystal coordinates; results are published at thebonhomme.com/benchmark/ as they are measured.
- Built Python bindings and the NRGsuite PyMOL plugin; zero-copy GPU/OpenMP batch scoring for high-throughput screens.
Lead programmer2014 − present
Najmanovich Research Group
- Principal software architect for the lab − own the NRG docking toolchain end to end across its Sherbrooke and Montréal eras.
Founder − Programmer − Research Scientist2023 − 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 researcherearlier
Najmanovich Research Group · 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.
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 scores FlexAIDΔS binding.
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.
NRGsuite
Python · PyMOL
open source
PyMOL plugin packaging the Najmanovich Research Group 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 & validation
FlexAIDΔS is validated on Astex Diverse 85 by self-docking and cross-docking with no crystal coordinates supplied, scoring the top pose by heavy-atom RMSD against the deposited ligand and by PoseBusters-style physical-plausibility checks. Shannon is validated on labelled entropy-collapse traces by detection sensitivity at fixed false-positive rate. The Astex campaign is in progress; measured results are published at thebonhomme.com/benchmark/ as they land, never before.
// publications
preprints & in preparation
- P1Morency L-P. FlexAIDΔS: entropy-driven molecular docking with a full ΔG = ΔH − TΔS statistical-mechanics score. Preprint / in preparation. 2026
- P2Morency L-P. Shannon: entropy-collapse detection for frontier LLM agents via the FlexAIDΔS configurational-entropy kernel. Preprint. 2026
peer-reviewed
- 01Morency 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
- 02Dion SP, Béliveau F, Morency L-P, Désilets A, Najmanovich RJ, Leduc R. Functional diversity of TMPRSS6 isoforms and variants expressed in hepatocellular carcinoma cell lines. Scientific Reports 8, 12562. 2018
- 03Chartier 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
- 04Gaudreault 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
- 05Leclerc J, Lefèvre T, Pottier F, Morency L-P, Lapointe-Verreault C, Gagné SM, Auger M. Structure and pH-induced alterations of recombinant and natural spider silk proteins in solution. Biopolymers 97(6), 337–346. 2012
invited talks & conference keynotes
- K1Morency L-P. The Impact of Conformational Entropy on the Accuracy of FlexAID in Binding Mode Prediction (part III) 3DSig · ISMB/ECCB 2019, Basel − selected oral talk (only ~3 non-PI speakers chosen per session). 2019
- K2Morency L-P. The Impact of Conformational Entropy on the Accuracy of FlexAID in Binding Mode Prediction (part II) ISMB 2018, Chicago − selected oral talk. 2018
- K3Morency L-P. The Impact of Conformational Entropy on the Accuracy of FlexAID in Binding Mode Prediction (part 1) 3DSig · ISMB/ECCB 2017, Prague − selected oral talk. 2017
- K4Morency L-P. NRGsuite: Fast, Flexible and Free PyMOL plugin for FlexAID. 3DSig · ISMB/ECCB 2015, Dublin − selected oral talk. 2015
- K5Morency L-P, Najmanovich RJ. Modelling conformational entropy in molecular docking − beyond the enthalpy-only score. PROTEO Annual Symposium, Québec (invited). 2019
// talks & teaching
workshopsHands-on docking with NRGsuite and FlexAID in PyMOL − graduate computational-biology methods.
invitedEntropy is not optional: why enthalpy-only docking gets the right answer for the wrong reason.
teachingTeaching assistant, biochemistry & structural bioinformatics − Université de Sherbrooke.
// technical skills
Languages
C++26C++20PythonSwiftCMakeBash
Scientific
Molecular dockingStatistical mechanicsFree-energy scoringNormal-mode / ENCoMShannon entropyHRV signal processing
Tooling
PyMOLOpenMPCUDA / GPUGitHealthKitCareKit
Practice
Reproducible buildsOpen-source maintenanceBenchmark designApache 2.0 / MIT
// awards & funding
Anthropic Open Source Program
Recognition for open-source contributions to the open scientific-software ecosystem − FlexAIDΔS, Shannon.
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).
Open-source contribution recognition
GitHub Arctic Code Vault Contributor; multi-year maintainer across the Najmanovich Research Group / Le Bonhomme Pharma stack.
// writing & advocacy
Book in progress − housing, organized crime, and harm reduction in Little Burgundy, Montréal: applied thermodynamics of a neighbourhood.
Drug of the Day − a rotating, rigorous harm-reduction pharmacology column at thebonhomme.com/drug-of-the-day/.