Set of useful HADDOCK utility scripts
Differentiable FRET distance distribution modeling 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.
Differentiable Cryo-EM map fitting in JAX
NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.
GNN-based protein structure refinement using JAX-differentiable kinematics to fit solution-state experimental data (SAXS/NMR).
A lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.
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.
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.
Differentiable HDX-MS prediction in JAX
JAX-native differentiable protein folding framework integrating experimental NMR constraints (RDCs) and biophysical "self-correction." Several Jupyter Notebooks visualize the concepts.
Integrative Refinement Engine for Differentiable Biophysics in JAX
Lightweight Crystallography profile simulation from protein coordinates, with Jupyter Notebook tutorials
Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.
Alessandro Nascimento Lab website
Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.
Repository containing files and scripts for molecular dynamics simulations of the transmembrane protein NPC1L1
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