Democapsid

Abstract

Capsids are the protein shells that protect the genetic material of viruses. The precise structural description of capsids informs how viruses assemble and evolve and is key to the development of antiviral targets. Most viruses form icosahedral capsids; among these, most adopt quasi-spherical shapes, and some form elongated architectures. However, elongated capsids have been understudied, despite their decoupling of width and length providing greater control over their packaging capacity, a feature of particular interest in capsid evolution and in virus-based biotechnological platforms. A key bottleneck is the lack of tools for the analysis and design of elongated viral capsids. To that end, this article introduces Democapsid as a versatile tool for generating coordinates of both quasi-spherical and elongated (and shrunk) icosahedral capsids, as well as for producing customizable graphical models and publication-quality figures. The underlying algorithm builds on the generalized geometrical theory of viral capsids and employs numerical methods to assemble capsid elements based on folding constraints. It includes parameters controlling protein tiling associated with the eight regular icosahedral lattices, elongation axes (5-fold, 3-fold, and 2-fold), sphericity, and discrete body length for prolate (extended) and oblate (shrunk) shapes. It is available as a JavaScript browser application, a Python package powering plugins for UCSF ChimeraX and Blender, and an R package for generating reproducible documents with embedded models. The code (MIT License) is available on GitHub. Democapsid will benefit both researchers and graphic designers by enabling the investigation and communication of research on viral capsids and other icosahedral compartments.