Derive ΔG for single residues from HDX-MS data

An interactive visual simulator for distance-based protein folding

Prediction of protein thermodynamic stability changes upon mutations through a Gaussian Network Model simulating protein unfolding behavior

A package for protein conformational ensemble analyses based on a differential geometry representation of protein backbones.

Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP).

Topological data analytic approach for discovering biophysical signatures in protein dynamics

Code for generating movies of the most relevant movement modes of proteins from their PDB files, using rigidity clustering analysis

PORCUPINEplot is a script developed to automate the generation of porcupine plots of PCA analysis.

C package that provides tools for correcting structural predictions of proteins (eg. from X-Ray Crystallography or AlphaFold) using X-ray small-angle scattering (SAXS) in solution

Predicting allosteric and active site residues in proteins with machine learning and protein sequence, structure and dynamics features

sbm-tools is a simple python package for creating, modifying, and maintaining input files for native Structure-Based Model simulations to be used with the popular simulation software GROMACS.

Program to calculate the most probable path between two equilibrium states of a biomolecule

Development of Python library for standardized generation and evaluation/characterization of protein structural ensembles.

protein dynamics analysis

A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission

A julia library for mode coupling analysis of protein simulations

Kern Lab website

Coarse-grained sticker spacer model of proteins