Galinter (Graph-based alignment of protein-protein interfaces) is a program for aligning non-covalent interactions at protein-protein interfaces. The method matches non-covalent interactions between different interfaces. The vector representations of van der Waals interactions and hydrogen bonds are aligned based on their geometry.
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Zhu H, Sommer I, Lengauer T, Domingues FS.
Alignment of Non-Covalent Interactions at Protein-Protein Interfaces.
PLoS ONE. 2008; 3(4): e1926.