The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs, and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules relies on a collection of automated scripts that work together to ensure each program runs independently, without interfering with others, thereby providing a transparent cross-platform solution without requiring specialized tools or admin privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform is made up of the Capsules environment with the SBGrid collection of structural biology applications, along with SBCloud which expands upon the platform by allowing the full SBGrid collection to be accessible utilising AWS cloud services. The SBGrid platform aligns with FAIR goals by enhancing the findability, accessibility, interoperability, and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.