Our first applications paper, published in Faraday Discussions in September, describes how we used cellPACK to generate and test several models of mature HIV particles.
Title: 3D molecular models of whole HIV-1 virions generated with cellPACK
Abstract: 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.
Authors: Graham T Johnson, David S Goodsell, Ludovic Autin, Stefano Forli, Michel F Sanner, & Arthur J Olson
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