Set of useful HADDOCK utility scripts
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.
Consensus-based visualisation of protein–protein interactions from MD trajectories
Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.
A lightweight Python library for simulating Small-Angle X-ray Scattering (SAXS) profiles from protein coordinates, with Jupyter Notebook examples.
Differentiable VAE framework for predicting protein structural ensembles (IDPs) consistent with SAXS and NMR data. Built on JAX/Flax.
GNN-based protein structure refinement using JAX-differentiable kinematics to fit solution-state experimental data (SAXS/NMR).
Integrative Refinement Engine for Differentiable Biophysics 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..
Alessandro Nascimento Lab website
Lightweight Crystallography profile simulation from protein coordinates
Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.
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