NSF SI2-SSE Project (2015-2018)

NSF Collaborative: SI2-SSE - A Plug-and-Play Software Platform of Robotics-Inspired Algorithms for Modeling Biomolecular Structures and Motions

This project is founded by the NSF ACI SI2-SSE under Grant No.1440581. The project brings together three teams of researchers from George Mason University (lead PI: Amarda Shehu, Computer Science), Catholic University of America (Erion Plaku, Computer Science), and University of Florida (Adrian Roitberg, Chemistry).

The project aims to develop a novel plug-and-play platform of open-source software elements to advance algorithmic research in molecular biology. The focus is on addressing the algorithmic impasse faced by computational chemists and biophysicists in structure-function related problems involving dynamic biomolecules central to our biology. The software platform resulting from this project provides the critical software infrastructure to support transformative research in molecular biology and computer science that benefits society at large by advancing our modeling capabilities and in turn our understanding of the role of biomolecules in critical mechanisms in a living and diseased cell.

The project addresses the current impasse on the length and time scales that can be afforded in biomolecular modeling and simulation. It does so by integrating cutting-edge knowledge from two different research communities, computational chemists and biophysicists focused on detailed physics-based simulations, and AI researchers focused on efficient search and optimization algorithms. The software elements integrate sophisticated energetic models and molecular representations with powerful search and optimization algorithms for complex modular systems inspired from robot motion planning. The plug-and-play feature of the software platform supports putting together novel algorithms, such as wrapping Molecular Dynamics or Monte Carlo as local search operators within larger robotics-inspired exploration frameworks, and adding emerging biomolecular representations, models, and search techniques even beyond the timeline of this project.

The project includes postdoctoral, graduate, and undergraduate. Expected contributions include:

  • Open-source software elements to conduct diverse structure-function studies in wildtype and variant protein sequences.
  • Support of well-established software, such as AMBER and Rosetta. Intuitive python interface to facilitate usage by dry- and wet-lab biologists, chemists, and biophysicists.
  • Plug-and-play feature to put together novel algorithms and so further drive algorithmic research in both AI and computational biophysics.
  • Active education of involved communities through workshops, tutorials, and software demos at widely-attended conferences and society meetings.

Updates, publication notifications, and software versions will be posted here.