Modeling and Interacting with the Visible Molecular Cell

PROJECT SUMMARY Integrative structural modeling of entire cells is a grand challenge actively being addressed by the structural biology community. The complexity and heterogeneity of structural models of entire cells poses several distinct challenges that are testing the current limits of technology and understanding. To tackle these challenges, we are developing the CellPACK Suite, a functional prototype of an entire integrative structural modeling pipeline. This pipeline allows users to gather and curate data from proteomics and structural databases, and to integrate this data into representative structural models that can be used for hypothesis generation and in-­silico testing. Our goal is to continue to develop, enhance, and harden this software, and to continue the application and validation of mesoscale modeling methods to biomedically relevant problems. The development will be driven by multiple collaborations with experimental and computational biologists with a focus on using mesoscale models to interpret and validate tomographic data, and on functional modeling of nucleoid structure in the context of entire bacterial cells and mitochondria. Throughout this work, we will work in the classic integrative structural biology mode, building models to interpret and reconcile 3D experimental tomographic data, and using models to infer the detailed molecular structure within tomographic data sets of limited resolution. We plan to expand and harden our growing toolbox for structural integrative modeling by developing new methods to incorporate specific interactions between molecules and working to increase the range of systems that are achievable. We are also committed to creating user-­friendly and targeted tools for the wider biological community and have created prototypes of software that allow facile model creation and hypothesis-­testing by non-­expert users. My laboratory brings 30 years of experience in gathering and integrating diverse biological data to depict the cellular mesoscale, and in the past 10 years, development of quantitative approaches to modeling the cellular mesoscale as computational infrastructure has progressed to the level where this is possible. Throughout this work, we have taken a practical, but exploratory, approach to methods development, building novel tools to address the underlying questions posed by our experimental collaborators, and then hardening the most effective tools to make them accessible to the larger computational biology community. We intend to create an accessible and effective toolbox for integrative modeling at the cellular mesoscale, driven by collaborative applications that span from atoms to cells.