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
Protein Internal Motion Analysis Based on Structural Compliance (SC) Mode Decomposition of Elastic Network Models (ENMs) Within a Robot Kinematics Framework
Elastic Network Model computation featuring GPU acceleration and parallel processing
Setup and run aMDeNM simulations with Python
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