allostery

Generate and perturb protein structural ensembles using the ExProSE algorithm

Predict allosteric pockets on proteins

A Python package to interactively compute, analyze and visualize protein allosteric communication (residue interaction) networks and delta-networks.

Reveal protein energy centers.

Protocol to model with allostery

RINFAIRE: Dynamic residue interaction networks from protein crystallographic multiconformer models

Network models of protein conformational entropy from dynamics

The Energetics of Molecular Adaptation in Transcriptional Regulation

Tools for studying long ranged —allosteric— effects in elastic networks (e.g. of proteins) on a mechanical basis.

ASDParser

Data and code for Computational Analysis of Dynamic Allostery and Control in the SARS-CoV-2 Main Protease

Paper I of "Statistical Pharmacology via Kakutani Dichotomy": the marginal drug Kakutani index (DKI) and the alpha_c = 1/2 criticality theorem for high-dimensional protein conformational ensembles. Paper (LaTeX/PDF), reproducible Python code, data and figures. DOI 10.5281/zenodo.23005921

Web service for simulations on a user-provided energy landscape

Paper II of "Statistical Pharmacology via Kakutani Dichotomy": the correlated Kakutani index (CKI), the 99.95% covariance dominance theorem (Szego rate in closed form) and spectral fingerprints of cryptic allostery. Paper (LaTeX/PDF), reproducible Python code, data and figures. DOI 10.5281/zenodo.23012217

Companion scripts for DMS data processing, dose-response curve fitting and figure reproduction (Stammnitz & Lehner, Nature Communications 2026)

Pure-PyTorch LAMMPS-AWSEM frustration analysis. 14-53x faster than frustrapy on a single GPU. Byte-comparable to frustratometeR.

Companion scripts for DMS data processing, dose-response curve fitting and figure reproduction ("The genetic architecture of an allosteric hormone receptor", Stammnitz & Lehner, Nature Communications 2026)

Paper V of Statistical Pharmacology via Kakutani Dichotomy: the chemical obstruction group Xi_beta^drug(S) = (Z/2Z)^{A_beta}, Borel-Cantelli tail order parameters, parity-cocycle invariance, and the relative-entropy staircase |A_beta| ln 2. Code, data, figure, LaTeX source and PDF.

Paper VI of Statistical Pharmacology via Kakutani Dichotomy: Wasserstein separation W_1(phi_+, phi_-) of broken phases under a Rieffel cone seminorm, certified to [0.229028, 0.229032]; the single-step scan barrier 5/12; discrete infinity-Laplacian cone geodesics; and a 2.77x FEP variance reduction for cooperative alchemical paths.

Kakutani–KMS theory of ligand-induced conformational phase transitions: integrating article of the Statistical Pharmacology via Kakutani Dichotomy series (Papers I–VII), with LaTeX source, PDF and verification script.