The growing role of open source software in molecular modeling

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Abstract
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high costs, and opaque systems that limit reproducibility, independent scrutiny, and scientific independence. This perspective advocates for permissively licensed open source software as a scientific and economic multiplier by reducing the duplication of effort, enabling scientific validation of modeling tools, and frictionless experimentation with new ideas. Coordinated, multi-project consortia, such as Open Force Field, Open Free Energy, OpenFold, and OpenADMET have formed to collaboratively build shared computational infrastructure and release all methods under permissive licenses. The success of these large-scale efforts requires organizational structures that extend beyond code. The Open Molecular Software Foundation (OMSF), a US nonprofit, serves as a domain-specific institutional home and fiscal sponsor. By providing governance, administrative infrastructure, and dedicated research software engineers, OMSF aligns incentives across academic and industrial stakeholders. This framework enables a synergistic ecosystem where projects interoperate to accelerate innovation, eliminate duplication, and ensure long-term software sustainability, thereby creating durable foundations that elevate the entire molecular modeling community.
Funding Information
  • NIH Office of the Director (R01GM132386)
  • Chan Zuckerberg Initiative (CZI EOSS5 2022-252547)