Journal
FARADAY DISCUSSIONS
Volume 169, Issue -, Pages 23-44Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/c4fd00017j
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Funding
- NSF [NSF 07576]
- NIH [P41 RR08605]
- QB3 Fellowship grant from the California Institute for Quantitative Biosciences
- qb3@UCSF
- UCSF School of Pharmacy, Mary Anne Koda-Kimble Seed Award for Innovation
- NATIONAL CENTER FOR RESEARCH RESOURCES [P41RR008605] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P50GM103368] Funding Source: NIH RePORTER
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As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology.
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