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CCP4: Software for Macromolecular X-Ray Crystallography

Phenix: A comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and electron cryo-microscopy data

PyMOL: a user-sponsored molecular visualization system

UCSF Chimera: a program for the interactive visualization and analysis of molecular structures and related data

Expasy: the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics