Graph Neural Networks for Structural Biology — Hands-on

Learn geometric deep learning for proteins, ligands, and complexes. Represent structures as graphs and surfaces, train 2D/3D equivariant GNNs for pocket/interaction/affinity tasks, and ship reproducible evaluation reports with clear baselines and error bars.

Graph Neural Networks for Structural Biology

Help Desk · WhatsApp

Session Index

Session 1 — Molecular/Protein Graphs & GNN Basics Session 2 — Protein Geometry: 3D, Surfaces & Equivariance Session 3 — Tasks: Pockets, Interfaces, Rescoring & Affinity Session 4 — Mini Capstone: Train → Evaluate → Report

Session 1

Fee: Rs 6300

Molecular/Protein Graphs & GNN Basics

Graphs for chemistry & proteins: atoms/residues, bonds/contacts, kNN & radius graphs

Theory

Message passing & attention; node/edge/global features

PyTorch Geometric DGL GraphConv/GAT/GIN

Featurization & loaders: PDB/mmCIF → graph datasets

AA props/SS/ASA ligand/metal flags

Session 2

Fee: Rs 8400

Protein Geometry: 3D, Surfaces & Equivariance

3D coordinates, frames & invariances; surface meshes & point clouds

triangulated surfaces MaSIF-like features

E (n) /SE (3) -equivariant GNNs for 3D proteins/complexes

EGNN/SE (3) -Transformer SchNet/DimeNet TFN (overview)

Efficiency & stability: batching, cutoffs, neighbor lists

mixed precision checkpointing

Session 3

Fee: Rs 11200

Tasks: Pockets, Interfaces, Rescoring & Affinity

Pocket/surface site prediction & residue-level function

classification/segmentation imbalanced data

PPI & protein–ligand: interface prediction, docking rescoring, affinity regression

PDBbind SAbDab/PP interfaces PR-AUC/RMSE/CI

Generalization & controls: scaffold/time splits, leakage checks

bootstraps calibration

Session 4

Fee: Rs 14000

Mini Capstone: Train → Evaluate → Report

Build a small GNN (PyG/DGL) for a chosen task (e.g., docking pose rescoring or pocket detection)

Theory + Practical

Benchmarking & deployment: ONNX/TorchScript export, inference profiling

baselines & CIs error analysis

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Graph Neural Networks for Structural Biology Training | 3D Equivariant GNNs for Pockets, Interfaces & Affinity

Graph Neural Networks for Structural Biology — Hands-on