Table 3.

Summary of publicly available software for the modeling of macromolecular structures.

Name	Hosted by	URL	Features	Availability	Reference
UCSF Chimera	Resource for biocomputing, visualization, and informatics at University of California, San Francisco, CA, USA	http://www.cgl.ucsf.edu/chimera/	Allows interactive visualization of macromolecular structures. Along with .pdb files, one can also import density maps, sequence alignments, and trajectories among other information. Python script plugins	For download on all major platforms	Pettersen et al. (28)
BioBlender	Science visulization unit, Consiglio Nazionale Delle Ricerche (CNR)	http://bioblender.eu	Built as an extension of blender, open-source 3D modeling software used for video games and animation, is able to display physical and chemical properties of a protein	For download on all major platforms	Andrei et al. (64)
Jmol	Various	http://jmol.sourceforge.net	Visualization of 3D protein structures in a variety of input formats including .pdb, can measure distances in Å. Great introductory animation at URL	Web applet	(65)

These software can import .pdb formatted files for viewing and/or manipulation and modeling.