Shared Resource: Molecular Modeling Facility

Research Inst Of Fox Chase Can Ctr, Philadelphia PA

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Abstract

COMPUTATIONAL/INFORMATICS SHARED RESOURCE: MOLECULAR MODELING FACILITY (MMF) PROJECT SUMMARY/ABSTRACT The Molecular Modeling Facility (MMF) is available to Cancer Center members to design and interpret experiments in all areas of cancer biology through the analysis of experimental and predicted three- dimensional structures of proteins and protein complexes. Under the direction of Roland Dunbrack, PhD (MT), and the effort of a 0.35 FTE Manager, the goals of the MMF are to provide services to Cancer Center members as follows: provide consultation to facilitate a more complete understanding of the structural biology of the biomolecules that are central to their research, including ongoing support for new hypothesis-driven experimentation that leads to a deeper mechanistic understanding of cancer related cellular pathways; provide structural biology consultation in cancer genetics; provide assistance and resources for the design of anti- cancer molecular therapeutics: make available in-house designed software and web server databases that perform complex modeling of proteins and analysis of protein complexes. MMF services were provided to 15 Cancer Center members in 2014. 87% of the Cancer Center members who utilized the MMF in 2014 had peer- review funded grants. 29 Cancer Center members from all 5 Research Programs used the MMF in the period 2011-2014. The specialized services performed by the Facility are not available from commercial companies. The Facility has proven its cost-effectiveness repeatedly throughout the years of its existence with structure- based design of more effective experiments and structurally informed interpretations of their results. As far as can be determined, the MMF is the only molecular modeling facility at any NCI-designated cancer center that provides molecular modeling and consultation to investigators as a Shared Resource. Some Cancer Centers have facilities that consist only of a workstation with molecular modeling software but no staff. Models are checked visually and with model evaluation software. Methods used in the Facility have been studied and validated extensively by Dunbrack?s research laboratory, which specializes not only in software development but also in high-throughput benchmarking of methods in protein structure prediction. Institutional funds ($352,000) were used in 2015 to purchase a cluster computer for Cancer Center members. The cluster has 480 processors, and will enable the MMF to undertake comprehensive, large-scale virtual screening of compounds for investigators. The MMF is supported by a Facility Advisory Committee (FAC) that meets at least annually. Recommendations from the FAC are directed to a governing Facility Parent Oversight Committee that serves to ensure that the MMF continues to have resources necessary to provide the highest quality services for Cancer Center members. Demand for services is expected to increase in the next cycle of the CCSG due to plans to recruit in all 5 Programs and new demand from Cancer Center members at TU.