Prediction of protein thermodynamic stability changes upon mutations through a Gaussian Network Model simulating protein unfolding behavior
Open source library to work with elastic network models
Predicting allosteric and active site residues in proteins with machine learning and protein sequence, structure and dynamics features
Setup, run and analyse Adaptive MDeNM simulations on CHARMM
Paper VII of Statistical Pharmacology via Kakutani Dichotomy: kakutani_pharma, a Python pipeline for Kakutani indices of MD conformational ensembles. Ledoit-Wolf regularized CKI with an exact three-way decomposition, split-trajectory null subtraction, within-half block bootstrap, and pocket-centred shell-scaling exponents. Validated on a synthetic
Paper VIII of Statistical Pharmacology via Kakutani Dichotomy: validation on real PDB ensembles (ubiquitin NMR, adenylate kinase), Isserlis bound and influence-function block selection, bootstrap coverage calibration. Code, data, paper.
Protein Internal Motion Analysis Based on Structural Compliance (SC) Mode Decomposition of Elastic Network Models (ENMs) Within a Robot Kinematics Framework
Paper IX of the Kakutani Dichotomy series: Notch-sparing gamma-secretase modulators for Alzheimer's disease, Schur-complement confinement of the Presenilin-1 catalytic block, infinity-Laplacian cone geodesics of processive tripeptide trimming, a dual-biomarker branching law, and allosteric rescue of familial PSEN1 alleles.
Elastic Network Model computation featuring GPU acceleration and parallel processing
Setup and run aMDeNM simulations with Python
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