Data and code for Computational Analysis of Dynamic Allostery and Control in the SARS-CoV-2 Main Protease
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Jul 22, 2020 - Python
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allostery
Here are 14 public repositories matching this topic...
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May 6, 2026 - Python
ASDParser
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Mar 10, 2024 - Python
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
reproducible-research numpy molecular-dynamics scipy python-package allostery structural-bioinformatics bhattacharyya-distance covariance-shrinkage normal-mode-analysis ledoit-wolf block-bootstrap high-dimensional-statistics finite-size-scaling elastic-network-models computational-pharmacology kakutani-dichotomy conformational-ensembles
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Sep 29, 2026 - Python
Alignment-independent distance correlation (dCor) analysis for pH-dependent activation of hENT3 (Tran & Lin, Biophys. J. 2026)
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Oct 27, 2026 - Python
Can ligand structure alone tell an allosteric modulator from an orthosteric one? A ChEMBL 37 benchmark showing how much apparent accuracy is split-scheme artefact and target look-up
benchmark machine-learning cheminformatics reproducible-research drug-discovery lightgbm rdkit allostery chembl dataset-bias
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Sep 30, 2026 - Python
Tools for studying long ranged —allosteric— effects in elastic networks (e.g. of proteins) on a mechanical basis.
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May 28, 2025 - Python
RINFAIRE: Dynamic residue interaction networks from protein crystallographic multiconformer models
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Oct 1, 2026 - Python
Pure-PyTorch LAMMPS-AWSEM frustration analysis. 14-53x faster than frustrapy on a single GPU. Byte-comparable to frustratometeR.
bioinformatics protein-structure cuda molecular-dynamics computational-biology pytorch gpu-acceleration drug-discovery frustration biophysics allostery structural-bioinformatics protein-folding awsem allosteric
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May 21, 2026 - Python
Reveal protein energy centers.
science proteins structural-biology protein-structure molecular-dynamics drug-design biophysics biomolecular-dynamics protein-design allostery protein-dynamics biomolecule allosteric-predictions biomolecular-simulation allosteric-site allosteric-pockets biomolecular-structures allostery-network allosteric-communication
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Oct 17, 2026 - Python
Network models of protein conformational entropy from dynamics
proteins molecular-dynamics computational-biology computational-chemistry molecular-simulation biophysics molecular-biology allostery protein-protein-interaction protein-dynamics protein-disorder conformational-changes allostery-network protein-thermostability allosteric-communication
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Oct 25, 2025 - Python
Predict allosteric pockets on proteins
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Mar 28, 2022 - Python
A Python package to interactively compute, analyze and visualize protein allosteric communication (residue interaction) networks and delta-networks.
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Jul 17, 2026 - Python
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