CellPACK: a Virtual Mesoscope to Model and Visualize Structural Systems Biology

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2014 Dec 2

PMID 25437435

Citations 77

Authors

Graham T Johnson

Ludovic Autin

Mostafa Al-Alusi

David S Goodsell

Michel F Sanner

Arthur J Olson

Affiliations

Soon will be listed here.

Abstract

cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.

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