😊 awesome-bioinformatics

A collection of papers studying bioinformatics using Deep Learning.

Please feel free to submit a pull request if you want to add good papers.

Class

• Stanford CS-279 Computational Biology: Structure and Organization of Biomolecules and Cells [Website]

Molecular/Protein Generation

• GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [Paper]
• Torsional Diffusion for Molecular Conformer Generation [Paper]
• Score-based Generative Models for Calorimeter Shower Simulation [Paper]
• Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models [Paper]
• A Score-based Geometric Model for Molecular Dynamics Simulations [Paper]
• Equivariant Diffusion for Molecule Generation in 3D [Paper]

Docking

• GNINA 1.0: molecular docking with deep learning [Paper]
• InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein−Ligand Interaction Predictions [Paper]
• AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands [Paper]
• Interpretable Drug Target Prediction Using Deep Neural Representation [Paper]
• Predicting drug–protein interaction using quasi-visual question answering system [Paper]
• DEEP LEARNING MODEL FOR FLEXIBLE AND EFFICIENT PROTEIN-LIGAND DOCKING [Paper]
• INDEPENDENT SE(3)-EQUIVARIANT MODELS FOR END-TO-END RIGID PROTEIN DOCKING [Paper]
• EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction [Paper]
• TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction [Paper]