Computational Biology Papers
Computational Biology paper note는 structure-based modeling, protein modeling, molecular generation, protein-ligand interaction, assay-aware label, domain-specific evaluation을 다룹니다.
이곳은 computational-biology paper를 읽기 위한 큰 선반입니다. Structure-based modeling papers와 Protein modeling papers 같은 좁은 묶음은 세부 주제가 필요할 때만 따라갑니다.
Reading Axes
- 어떤 object를 모델링하는가: protein, molecule, ligand, pocket, complex, pose, assay record, sequence region?
- 중심 route가 무엇인가: sequence-based modeling, molecular and ligand modeling, interaction modeling, structure-based modeling?
- contribution이 AI method, domain workflow, benchmark, dataset, evaluation protocol 중 무엇인가?
- molecule standardization, protein-family split, scaffold split, assay semantics, leakage risk가 explicit한가?
- paper가 method quality를 benchmark artifact나 domain shortcut과 분리하는가?
Sub-Buckets
| Bucket | Use for | Notes |
|---|---|---|
| Structure-based modeling papers | docking, pose quality, scoring, conformers, virtual screening | PoseBusters |
| Protein modeling papers | protein representation, structure, antibody/protein interaction | MEET, Multi-scale antibody binding |
| Generative model papers | molecule/protein generation when generation is the strongest claim | Molexar |
Active Notes
| Paper note | Main route | 여기 두는 이유 |
|---|---|---|
| Chemical Dice Integrator | molecular representation learning | multimodal chemistry teacher distilled into a deployable SMILES-only embedding model |
| PoseBusters | structure-based evaluation | pose plausibility and docking evaluation |
| AlphaFold2 | protein structure prediction | MSA-pair architecture, geometric structure module, recycling, and confidence |
| AlphaFold3 | biomolecular complex prediction | diffusion-based joint structure prediction for proteins, nucleic acids, ligands, ions, and modified residues |
| ProteinMPNN | protein inverse folding | structure-conditioned sequence design for fixed protein backbones |
| NequIP | molecular and materials potentials | E(3)-equivariant interatomic potential for energy-force modeling |
| MEET | protein and geometric modeling | equivariant peptide modeling |
| Multi-scale ML for Antibody-Antigen Binding | protein interaction modeling | antibody-antigen binding evaluation |
| Molexar | molecular generation | molecule-focused generation and representation |
Concepts
- Computational Biology
- Data and Evaluation
- Structure-based modeling
- Interaction modeling
- Structure-based drug discovery
- Protein modeling
- Molecular modeling
- Leakage