Amelie's Projects
Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer)
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
Implementation of Alphafold3 in Pytorch
Config files for my GitHub profile.
Guiding diffusion models for antibody sequence and structure co-design with developability properties.
Resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"
Boltzmann Generators and Normalizing Flows in PyTorch
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations (EMNLP 2023)
Bi-Directional Equivariant Long-Range DNA Sequence Modeling
ChatGPT for Drug Discovery
Community wiki for computational longevity topics.
Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.
Adapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.
Code for the paper Iterated Denoising Energy Matching for Sampling from Boltzmann Densities.
Diffusion model based protein-ligand flexible docking method
Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
A Euclidean diffusion model for structure-based drug design.
š§¬ Generative modeling of regulatory DNA sequences with diffusion probabilistic models šØ
DrugAssist: A Large Language Model for Molecule Optimization
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