Model for predicting micro-millisecond motions from protein sequence and/or structure

Derive ΔG for single residues from HDX-MS data

An interactive visual simulator for distance-based protein folding

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

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

Compact sequence-only neural propagator for protein torsion dynamics. 2.39x lower JSD than Microsoft Timewarp at 3000x fewer parameters. pip install alphadynamics.

Reveal protein energy centers.

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

Compute differential geometry descriptors for protein conformational ensembles

open-source python package for accessing and analyzing NMR data

Topological data analytic approach for discovering biophysical signatures in protein dynamics

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

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

Network models of protein conformational entropy from dynamics

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

Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.

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