From wireframes to immersive reality: a historical perspective on molecular visualization software

The evolution of molecular visualization software represents a pivotal yet often underappreciated dimension of computational structural biology and bioinformatics. As the scale and complexity of structural datasets increase, spanning from cryo-electron microscopy reconstructions to proteome-wide AI-predicted models, visualization tools have become essential for data interpretation, hypothesis generation, and effective scientific communication. Widely used platforms such as PyMOL, UCSF Chimera, and emerging virtual reality environments reflect decades of progressive innovation driven by advancements in computational hardware, graphics rendering, and algorithm development. This review traces the historical development of molecular graphics software, from early vector-based applications like FRODO and O, through interactive tools including RasMol and VMD, to modern real-time 3D visualization frameworks. We highlight key technological milestones and design principles that continue to shape contemporary software architectures, underscoring the interdisciplinary collaborations among chemists, structural biologists, and computer scientists that have propelled the field. Given the current integration of artificial intelligence, immersive visualization, and cloud computing in structural bioinformatics workflows, revisiting this topic provides critical context for guiding the design of more intuitive, scalable, and accessible visualization platforms. By documenting and critically analyzing this trajectory, the present work aims to honor the foundational contributions to molecular graphics while positioning the field as a dynamic and integral component of future bioinformatics research and computational discovery.