Computational Biophysics Scientist: Protein Dynamics & ML

Astera Institute; Emeryville (CA); On-site; USD 150,000 - 210,000; Full time

Benefits offered by this job

Benefits summary

Job summary

Astera Institute's Prism program seeks a scientist to advance open infrastructure for studying protein dynamics, integrating experimental data with ML to model sequence-structure-function relationships. You will develop scalable pipelines and collaborate with experimental partners to ground computational representations in real measurements.

The role offers cross-disciplinary collaboration with ML researchers, software engineers, and program staff across Radial, Astera, and partner institutions,

Qualifications

• PhD in bioinformatics, computational biology, ML, or related field.
• Strong understanding of protein structure and function.
• Demonstrated experience building large bioinformatic pipelines and managing high-dimensional datasets.
• Proficiency in fine-tuning or modifying ML models (e.g., transformer-based architectures).
• Familiarity with protein language models (ESM, AlphaFold) is a plus.
• Collaborative, team-oriented mindset with the ability to drive research questions from conception to execution.

Responsibilities

• Build ensemble-aware protein representations that integrate PLM and LLM embeddings with experimentally derived structural heterogeneity for functional prediction
• Design, develop, and maintain large-scale bioinformatic pipelines capable of processing and managing complex, high-dimensional datasets
• Fine-tune or architect ML models to capture sequence-structure-function relationships, with a focus on dynamic and conformational features
• Synthesize diverse data sources spanning evolutionary history, binding affinity, allostery, and functional annotations to improve model performance and biological relevance
• Collaborate closely with experimental partners to ground computational representations in real biological measurements and ensure models are continuously refined against experimental ground truth
• Contribute to the broader Prism infrastructure, helping establish community-wide standards and tools for dynamic structural biology

Skills

Protein structure knowledge

Bioinformatics pipelines

ML model fine-tuning

Protein language models

Collaboration

Education

PhD in bioinformatics or related field

Tools

PyTorch

Transformers

AlphaFold

Job description

Astera Institute's Prism program seeks a scientist to advance open infrastructure for studying protein dynamics, integrating experimental data with ML to model sequence-structure-function relationships. You will develop scalable pipelines and collaborate with experimental partners to ground computational representations in real measurements.

The role offers cross-disciplinary collaboration with ML researchers, software engineers, and program staff across Radial, Astera, and partner institutions,