Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Role in this project:
ML Engineer Contributions:2 reviews, 90 commits, 3 PRs in 1 year 3 months
Contributions summary:Sachin implemented several execution wrappers for external tools such as HHBlits, HHSearch, and Jackhmmer, which are essential for generating multiple sequence alignments (MSAs) and homologous protein searches. They also developed a Kalign wrapper for template sequence alignment, a crucial step in template-based protein structure prediction. Further contributions include the creation of feature transformations and data pipelines, specifically for integrating MSAs and template features into the AlphaFold 2 pipeline, showing significant involvement in the feature engineering aspect of the project.
gpupytorchprotein-structurealphafold2
Contributions:6 pushes, 3 branches in 1 year 2 months