CAREER: Designing Systems for Molecular Query-Retrieval and Molecular Informatics

San Francisco State University, San Francisco CA

Investigators

Abstract

The ability to manage and efficaciously reason with molecular structural information has enormous impact both for bio-chemical research as well as for the discovery of new and more efficacious therapeutics. The advent of technologies like NMR, Crystallography, and Combinatorial Chemistry, allow us today to generate unprecedented amounts of information at the molecular structural level. However, the capacity to generate molecular structural data far exceeds our ability to effectively manage, query, and assimilate it at the state-of-the-art. From a computer science perspective, molecules are complex, multidimensional entities which present critical challenges for effective and efficient design of representation, retrieval, modeling, and interaction techniques. In this context, this research focuses on three challenges: (1) Designing techniques for representation and similarity-based matching of molecules, (2) Development of indexing strategies for molecular query-retrieval, and (3) Designing knowledge environments for discovery of therapeutics. The specific research innovations include design of standard coordinate systems to represent highly complex molecular surfaces, developing efficient information matching and retrieval techniques for comparing molecules, and design of integrated information management of molecular structures and biological properties including the development of user-data interaction techniques and algorithms for context supportive access to meta-knowledge. Broader Impact: Techniques and systems developed as part of this research will be made publicly available and allow fundamental advancements in management, exploration, analysis, and reasoning with molecular information. This has the potential to introduce ground breaking advancements in areas like drug/therapeutics discovery and thus is critical to the society at large. Furthermore, this research will establish "Molecular Query-Retrieval and Molecular Informatics" as an integral part of computer science research in information management, retrieval, analysis, and assimilation. This will allow computer scientists to participate and advance a critical and new interdisciplinary area. Finally, the education and outreach component will (a) develop models to enhance research experience and productivity of students, (b) providing exposure to computer science at the grassroots-level through novel interactions with students and teachers at K-12 levels, and (c) broaden participation by mentoring women and minority students.