The Evolution of Protein Technologies

text: Katrine Anker-Nilssen photo: Supplied

During his PhD research exchange placement at the International Livestock Research Institute (ILRI) in Nairobi, Kenya, Isaac Omara seized the opportunity to attend an intensive one-week workshop on advanced structural biology and computational modeling. “The training provided me with practical skills in modern computer tools to visualise protein structures, understand highresolution images of them, and test small chemical candidates on proteins for potential drug discovery,” explains Isaac. “It was an eye-opening experience that not only introduced me to protein structural analysis and computational modeling, but also connected me with a vibrant network of African and international scientists committed to tackling pressing health challenges through cutting-edge techniques.”

Isaac gained hands-on experience with advanced structural biology tools such as AlphaFold, PyMol, and ChimeraX – innovative resources that are revolutionising our understanding of proteins and design interventions. “I was particularly excited to see how these techniques could be applied not only to drug discovery, but also to vaccine target validation, which aligns closely with my PhD research on Rift Valley fever virus,” he says.

Acquiring skills in AlphaFold, an advanced AI tool developed by Google DeepMind, was particularly valuable for Isaac. This tool can predict the 3D structure of proteins based solely on their amino acid sequences, which is crucial for understanding protein function and identifying vaccine targets. “Although my PhD primarily featured AlphaFold and PyMol, this workshop enriched my understanding of the evolution of structural biology from experimental methods like X-ray crystallography and Cryo-EM to the emergence of AI-driven tools like AlphaFold,” Isaac notes. “This context clarified how my project fits within the broader scientific narrative and deepened my appreciation of how my work builds on decades of advancements in the field.”

The skills Isaac acquired during the workshop directly enhance his PhD research, which focuses on genomic evolution and vaccine target discovery for Rift Valley fever virus. “My project involves analyzing RVFV genomes from African outbreaks to identify critical mutations and predicting B-cell and T-cell epitopes for potential human vaccine development,” he explains. “The new skills I gained will enable me to model these viral proteins in 3D, offering a clearer perspective on how mutations may influence protein shapes and how epitopes are exposed to the immune system. This structural insight will improve the accuracy of my vaccine target predictions and help me validate them more confidently.”

One of the most challenging aspects of the training was interpreting the complex protein structures after processing them through AlphaFold. “Generating the models was straightforward; however, analysing intricate structural details – such as active sites, binding pockets, or ligands – required critical thinking and guidance from the facilitators,” Isaac elaborates.

By introducing new knowledge and skills in structural biology and protein modeling into CERI’s pathogen genomics work, Isaac adds a vital dimension to research efforts aimed at better understanding viral evolution and identifying potential vaccine targets. This can also support the training of other researchers in Africa to utilise these tools effectively. “The methods strengthen CERI’s initiatives by linking genomic surveillance with structural biology and computational modeling for vaccine and therapeutic design, positioning CERI not only to respond to epidemics and pandemics but also to drive solutions against them.

“I plan to share the skills I’ve acquired through both formal and informal channels to maximise impact. This includes presenting at CERI’s working group and sharing ideas for collaborative projects – ensuring that techniques like 3D protein prediction, visualisation, and docking become accessible to others working on diverse pathogens. Beyond CERI, I will engage with the broader African genomics community through conferences and collaborative networks.”

In addition, during the workshop, Isaac initiated a mentorship with Dr. Emmanuel Nji, CEO and Cofounder of Biostruct-Africa, focusing on AlphaFold and structure-guided epitope mapping to support his PhD work on Rift Valley fever virus. “Without a doubt, my top takeaway was learning how structural biology tools can transform genomic data into actionable insights that address global health challenges,” he concludes.