prescient-design/lobster
Jan 2025 – Feb 2025
2 Months active
Languages Used
PDBPythonJinja
Technical Skills
Antibody EngineeringBioinformaticsPDB File ManipulationProtein Structure AnalysisPyTorchPython
Frédéric Dreyer
PROFILE
Frédéric Dreyer
Over a two-month period, contributed to the prescient-design/lobster repository by developing two core features focused on antibody modeling and protein language models. Built the Predict Fv PDB Formatter, which processes antibody variable fragments by handling heavy and light chains, generating homodimer sequences, and ensuring correct chain identifiers and residue numbering in PDB files, all implemented and tested in Python. Subsequently integrated the ESMSC-small model into LobsterPMLM, enabling support for Synthyra/ESMplusplus_small with optional bfloat16 precision and a new dataset embedding method. Leveraged skills in PyTorch, deep learning, and PDB file manipulation to enhance model compatibility and workflow reliability.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
2Total
Bugs
0
Commits
2
Features
2
Lines of code
1,969
Activity Months2
Your Network
34 peopleShared Repositories
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thomasMember
Ed WagstaffMember
freyn6Member
Colin GrambowMember
ismaia11Member
Jen HofmannMember
Karina ZadorozhnyMember
Joseph KleinhenzMember
Work History
February 2025
1 Commits • 1 Features
Feb 1, 2025February 2025 — Prescient Design Lobster: Implemented ESMSC-small model integration in LobsterPMLM, enabling loading and utilization of Synthyra/ESMplusplus_small, optional bfloat16 precision, and a new dataset embedding method. Adjustments were made to accommodate the ESMSC-small model type. A minimal ESMSC-small implementation was delivered (commit 0d0285628ee2fa0065a9fadce646a8036f2ed9c5) (#37). This work broadens model compatibility, accelerates experimentation, and enhances embedding quality for downstream tasks.
1 Commits • 1 Features
Feb 1, 2025February 2025 — Prescient Design Lobster: Implemented ESMSC-small model integration in LobsterPMLM, enabling loading and utilization of Synthyra/ESMplusplus_small, optional bfloat16 precision, and a new dataset embedding method. Adjustments were made to accommodate the ESMSC-small model type. A minimal ESMSC-small implementation was delivered (commit 0d0285628ee2fa0065a9fadce646a8036f2ed9c5) (#37). This work broadens model compatibility, accelerates experimentation, and enhances embedding quality for downstream tasks.
February 2025
January 2025
1 Commits • 1 Features
Jan 1, 2025January 2025 monthly summary for prescient-design/lobster focusing on feature delivery and code quality improvements in the antibody modeling pipeline.
January 2025
1 Commits • 1 Features
Jan 1, 2025January 2025 monthly summary for prescient-design/lobster focusing on feature delivery and code quality improvements in the antibody modeling pipeline.
Activity
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Quality Metrics
Correctness85.0%
Maintainability80.0%
Architecture85.0%
Performance70.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
JinjaPDBPython
Technical Skills
Antibody EngineeringBioinformaticsDeep LearningHugging Face TransformersMachine LearningNatural Language ProcessingPDB File ManipulationProtein Structure AnalysisPyTorchPython
Repositories Contributed To
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