Shafayat Ahmed just completed his internship in Software Engineering with the Protein Modeling and Simulation team at BIOVIA. The overall goal of Shafayat’s project was to develop a modern, automated and reproducible antibody viscosity prediction workflow in BIOVIA Discovery Studio Simulation. Shafayat leveraged the ANARCII framework and DeepViscosity to improve antibody viscosity prediction directly from protein sequences, eliminating the need for explicit 3D structure generation. He helped develop and integrate the workflow into BIOVIA Pipeline Pilot, creating a faster, more reproducible, and reliable pipeline for antibody sequence processing, viscosity prediction, downstream analysis, and result visualization.
I really enjoyed working at the intersection of computational biology, machine learning, and software engineering, and appreciated the guidance and support from mentors Defne Ozgulbas and Rohith Mohan, and rest of the BIOVIA Life Sciences Modeling and Simulation team throughout my internship.
— Shafayat Ahmed
Check out the video to learn more about Shafayat’s journey and his experience developing scientific software solutions at BIOVIA, Dassault Systèmes.
Dr. Defne G. Ozgulbas is an R&D Software Engineering Specialist on the Protein Modeling and Simulation team at BIOVIA, Dassault Systèmes. She received her Ph.D. in Biophysics and Computational Biology from the University of Illinois at Urbana-Champaign, where she was a Beckman Graduate Fellow in the Theoretical and Computational Biophysics Group. Her doctoral research focused on biomolecular modeling, protein design and engineering, and protein-membrane interactions using advanced molecular dynamics simulations. At BIOVIA, she develops modeling and simulation tools in BIOVIA Discovery Studio. Her work spans simulation methods, biologics and antibody workflows, developability assessment, and the intersection of AI/ML in these areas.