B. Y. Chen, V. Y. Fofanov, D. M. Kristensen, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs,” in Pacific Symposium on Biocomputing, Hawaii, USA, 2005.
PDF preprint: http://kavrakilab.org/publications/chen-fofanov2005algorithms-for-structural.pdf