BIOVIA is excited to announce our growing collaboration with UC Berkeley’s Master of Molecular Science and Software Engineering (MSSE) program. This partnership brings together our industry expertise with emerging talent in computational science, creating opportunities for innovation in addressing real-world challenges in molecular sciences. Our collaboration began with a capstone project in Spring 2024 and is now expanding into its second year with plans for continued engagement with this exceptional program.
Our initial collaboration featured a successful project where a team of UC Berkeley MSSE students developed CalMPNN, a Python module that integrates advanced neural network models for protein sequence design and stability prediction. The team unified two sophisticated approaches from the Baker and Kuhlman labs into a coherent framework with a simplified interface that streamlined workflows. They ensured scientific integrity by implementing comprehensive testing protocols that validated their implementation across diverse use cases. Their work improved the practical application of these computational tools by providing a more intuitive means of interacting with the underlying algorithms. As project mentors, myself and my colleague, Reed Harrison, provided guidance throughout this journey, helping the team implement software engineering best practices that deliver consistent results across both CPU and GPU computing environments.
Building on this success, we’re excited to be underway with our second year of sponsorship for another MSSE capstone project. These collaborations not only provide valuable real-world experience for Berkeley students but also enhance BIOVIA’s capabilities by incorporating fresh perspectives and innovative approaches to computational challenges in drug discovery.
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Rohith received his Ph.D. in Bioengineering from University of California, Riverside. As part of his doctorate research he studied the complement system and the molecular basis of immune-related diseases by using MD simulations for mechanistic studies, peptide design, and virtual drug screening. He joined BIOVIA in 2018 as part of the Discovery Studio R&D team for the development of modeling and simulation tools for drug design and discovery. He currently leads the Protein Modeling and Simulation team in Discovery Studio where he works on force field parameterization, free energy methods, simulation methods, and the intersection of AI/ML in these areas. Rohith is also a fellow of the BIOVIA Science Council.