Forward-Deployed ML Engineer – Cofolding at Apheris

Seniority in posting: experienced

Language

Setup: Remote
Location: Berlin
Type: Full-time
Level: senior
Posted: Jul 7, 2026

Description

Apheris is hiring a Senior ML Engineer to advance structural biology models for drug discovery. The role focuses on fine-tuning and extending foundational models such as OpenFold, Boltz-2, and ESMFold; developing protein complex and binding-affinity prediction systems; designing scalable training, inference, and deployment pipelines; and delivering customer-facing case studies. The position requires deep experience with production machine learning, protein structure or drug-discovery applications, and modern MLOps, with a remote-first arrangement and early-stage virtual share options.

Required Skills

Protein structure prediction
Model fine-tuning
MLOps
Data preprocessing
Model deployment
Federated learning

Additional Information

Required Previous Experiences: Experience building and training contemporary machine learning models at scale, including AlphaFold, OpenFold, and Boltz, with modern MLOps tooling.
Experience applying machine learning to real-world protein structure or drug discovery problems.
Experience designing scalable data preprocessing, training, and evaluation workflows for structural biology.
Preferred Qualifications: Experience with federated learning, privacy-preserving machine learning, or privacy-preserving model training.
Publication in machine learning or biology journals or conferences.