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.

protein dynamics analysis

A julia library for mode coupling analysis of protein simulations

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

Coarse-grained sticker spacer model of proteins

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

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

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

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

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

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

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

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

Kern Lab website

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

An interactive visual simulator for distance-based protein folding

Derive ΔG for single residues from HDX-MS data