By Rita Okoye
In the world of cutting-edge science, and the era of advanced biomolecular simulations, computational resources are as indispensable as physical laboratories. The rapid growth of computer-aided biological research, driven by advancements in computational power, is reshaping fields like drug discovery, materials science, and biotechnology. Dr. Abeeb Abiodun Yekeen, an expert in computer-aided drug discovery, is calling for Nigeria to invest in high-performance computing (HPC) to unlock the potential of computational research for national development.
Dr. Yekeen holds a PhD from the University of Science and Technology of China, where he conducted research in the Laboratory of Computational Biology. Since 2023, he has been a postdoctoral researcher at the University of Texas Southwestern Medical Centre, working at the interface of cancer drug discovery and computational structural biology. With nearly a decade of experience in biomolecular modelling and simulation, Dr. Yekeen highlights the critical need for HPC resources in Nigerian academic and research institutions.
One of his recent studies, titled “CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses” and published in the Computational and Structural Biotechnology Journal, introduces CHAPERONg, a software he developed to automate molecular dynamics (MD) simulations with the GROMACS engine. “MD simulations are vital in understanding biomolecular interactions at the atomic level,” explains Dr. Yekeen. “These insights are crucial for advancing drug discovery, materials science, and biotechnology.”
“GROMACS is arguably the most common MD simulation engine for biomolecules. This is due to it being free, open-source, fast, versatile, and extensive. It also has a huge community of users and developers, making it popular among computational scientists. However, having engaged in several studies that utilized GROMACS MD simulations, I observed the need for a tool that automates the repetitive and manual steps involved in setting up and running the simulations,” he explains. “I developed CHAPERONg to automate and streamline the running and analyses of MD simulations, empowering scientists to more efficiently model biomolecules, design therapeutics, and investigate biomolecular interactions.” Explaining further, he says “Considering the huge number of users of GROMACS, CHAPERONg practically solves a big problem for many computational biochemists.”
“However, such simulations are computationally intensive,” Dr. Yekeen notes.” They require HPC resources to execute advanced modelling, run long simulations, and deliver results efficiently. Without adequate HPC infrastructure, researchers face delays, technical bottlenecks, and limited opportunities for groundbreaking discoveries.”
“HPC is a cornerstone of modern scientific research and innovation,” he argues. Dr. Yekeen envisions a Nigeria where HPC is a central pillar of academic and research institutions. By establishing national HPC centres, the country can provide researchers with the tools they need to compete and contribute globally. “HPC is not a luxury—it’s a necessity for modern science,” he asserts. “Nigeria has brilliant minds capable of contributing to global science, but we need the infrastructure to unlock this potential”, he concludes.