computational-structural-biology

Set of useful HADDOCK utility scripts

Differentiable FRET distance distribution modeling in JAX

Differentiable Cryo-EM map fitting in JAX

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

Generate realistic synthetic 3D Cryo-EM densities from structural models for testing algorithms and training ML models.

NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.

A lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.

GNN-based protein structure refinement using JAX-differentiable kinematics to fit solution-state experimental data (SAXS/NMR).

Differentiable EPR/DEER distance distribution modeling in JAX

Differentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and scanning lag.

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

Consensus-based visualisation of protein–protein interactions from MD trajectories

Differentiable VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.

Integrative Refinement Engine for Differentiable Biophysics in JAX

JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.

Differentiable HDX-MS prediction in JAX

Lightweight Crystallography profile simulation from protein coordinates, with Jupyter Notebook tutorials

Alessandro Nascimento Lab website

Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.