BC-Design: A Biochemistry-Aware Framework for Inverse Protein Design
Evaluating how biochemical conditioning shapes protein sequence design through controlled experiments and molecular dynamics analysis.
Overview
BC-Design combines protein structure with biochemical information to guide sequence design. I collaborated remotely with Xiangru Tang, a PhD student at Yale University, on the experiments, analysis, and manuscript revisions for this work.
My contribution
- Conducted biochemical feature masking and perturbation experiments to assess which information drives sequence recovery.
- Compared input conditions to distinguish information derived from the target sequence from conditions available during design.
- Evaluated enzyme and antibody design applications using computational metrics, and analyzed molecular dynamics trajectories of PGK complexes.
- Wrote responses to reviewers and revised the manuscript to incorporate the additional experiments and clarify the role of biochemical conditioning.
Research focus
A central part of my contribution was making the input conditions explicit. Comparing native biochemical information, predicted fields, and masked inputs helped separate sequence reconstruction from design with limited information. The revision also examined how sequence recovery relates to structural and application-specific evaluation.
Manuscript and code
BC-Design: A Biochemistry-Aware Framework for Inverse Protein Design
Joint first author on the revised manuscript. In revision at Cell Systems.