Colorado State University

The Computational Biochemistry Laboratory focuses on understanding molecular regulation by  exploring protein interactions and macromolecular assemblies. We combine High-Performance-Computing (HPC) and Machine Learning (AI/ML) to create computational models of bimolecular complexes and systems in multiple scales, form quantum chemistry to systems biology. Our models are informed by a deep understanding of the biological and physiological context of the target systems, and focus on providing mechanistic insight.

We are currently working on protein complexes that mediate cell adhesion, and enzymatic complexes that regulate metabolic networks. Specifically, we are exploring how molecular interfaces define binding affinity and mechanical resilience, and how these interfaces affect the biological function of protein complexes, such as a TCR:MHC interface, a scaffolding module for bacterial adhesion in biofilms, or a metabolic enzyme regulating energy flow. 

The methods used in our group change from project to project. From ML/AI models based on SciPy/PyTorch/TensorFlow in data science-oriented projects dealing with hundreds of TB of data, to molecular modeling and dynamics in structural biology and molecular design-oriented projects, to software development in C++/Python for HPC-oriented methods development projects. We balance computational data generation and analysis with integration of  large-scale experimental data

Ultimately, we share a passion for exploring biology with computational models, and are always looking for a new angle and a new question to be asked!