Modeling Macromolecular Complexes: A Journey Across Scales - Modeling in Computational Biology and Biomedicine - page 40

compatch
http://cgal.inria.fr/abs/compatch
compatch is the program comparing two binding patches, either from a geometric
or topological standpoint, based on the shelling tree computed by vorpatch. Refer to
Sect. 1.2.5 .
voratom
http://cgal.inria.fr/abs/voratom
voratom is a software suite meant to create and explore toleranced models. The
applications provided allow performing the segmentation of a 3D density map,
creating a toleranced model from occupancy volumes, exploring the Hasse diagram
of a toleranced model, and checking the complexes associated with nodes of the
Hasse diagram against 3D templates.

SITUS
http://situs.biomachina.org/
SITUS is a package for modeling atomic resolution structures by combining low-
resolution density maps (electron microscopy, tomography, or small angle X-ray
scattering) on the one hand, and atomic models on the other hand.

Acknowledgements Joel Janin is acknowledged for insightful discussions.

List of Acronyms

PDB Protein Data Bank

cryoEM cryo-electron microscopy

TAP Tandem Affinity Purification

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