Amelie's Projects
Improving ProteinMPNN sequence design and selection with kernel methods.
Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer)
Force aggregation code aimed at coarse-grained molecular dynamics
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.
Improved antibody structure-based design using inverse folding
Resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"
Bio Electric Tissue Simulation Engine: Mark I
Bio Electric Tissue Simulation Engine Environment.
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
Single-cell bioelectricity web app.
ChatGPT for Drug Discovery
Fine-tuning Galactica and Gemma to operate on SMILES. Integrates into a molecular optimization algorithm.
A generative model for programmable protein design
Making Protein folding accessible to all!
Community wiki for computational longevity topics.