A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-540, 1995.
DOI : 10.1016/S0022-2836(05)80134-2

C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells et al., CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-1108, 1997.
DOI : 10.1016/S0969-2126(97)00260-8

F. Bernstein, T. Koetzle, G. Williams, E. M. Meyer, . Jr et al., The protein data bank: A computer-based archival file for macromolecular structures, Archives of Biochemistry and Biophysics, vol.185, issue.2, pp.584-591, 1978.
DOI : 10.1016/0003-9861(78)90204-7

A. Godzik, J. Skolnick, and A. Kolinski, Regularities in interaction patterns of globular proteins, "Protein Engineering, Design and Selection", vol.6, issue.8, pp.801-810, 1993.
DOI : 10.1093/protein/6.8.801

A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz, 1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap, Journal of Computational Biology, vol.11, issue.1, pp.27-52, 2004.
DOI : 10.1089/106652704773416876

W. Xie and N. V. Sahinidis, A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem, Journal of Computational Biology, vol.14, issue.5, pp.637-654, 2007.
DOI : 10.1089/cmb.2007.R007

D. A. Pelta, J. R. González, and M. M. Vega, A simple and fast heuristic for protein structure comparison, BMC Bioinformatics, vol.9, issue.1, p.161, 2008.
DOI : 10.1186/1471-2105-9-161

R. Andonov, N. Malod-dognin, and N. Yanev, Maximum Contact Map Overlap Revisited, Journal of Computational Biology, vol.18, issue.1, pp.27-41, 2011.
DOI : 10.1089/cmb.2009.0196

URL : https://hal.archives-ouvertes.fr/inria-00536624

N. Malod-dognin, M. L. Boudic-jamin, P. Kamath, and R. Andonov, Using Dominances for Solving the Protein Family Identification Problem, In Algorithms in Bioinformatics, vol.33, issue.4, pp.201-212, 2011.
DOI : 10.1093/nar/gki524

URL : https://hal.archives-ouvertes.fr/inria-00609432

I. Wohlers, N. Malod-dognin, R. Andonov, and G. W. Klau, CSA: comprehensive comparison of pairwise protein structure alignments, Nucleic Acids Research, vol.40, issue.W1, pp.303-309, 2012.
DOI : 10.1093/nar/gks362

URL : https://hal.archives-ouvertes.fr/hal-00667920

N. Malod-dognin and N. Przulj, GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity, Bioinformatics, vol.30, issue.9, pp.1259-1265, 2014.
DOI : 10.1093/bioinformatics/btu020

K. L. Clarkson, Nearest-neighbor searching and metric space dimensions

F. Moreno-seco, L. Mico, and J. Oncina, A modification of the LAESA algorithm for approximated k-NN classification, Pattern Recognition Letters, vol.24, issue.1-3, pp.47-53, 2003.
DOI : 10.1016/S0167-8655(02)00187-3

M. L. Mico, J. Oncina, and E. Vidal, A new version of the nearest-neighbour approximating and eliminating search algorithm (AESA) with linear preprocessing time and memory requirements, Pattern Recognition Letters, vol.15, issue.1, pp.9-17, 1994.
DOI : 10.1016/0167-8655(94)90095-7

P. Rogen and B. Fain, Automatic classification of protein structure by using Gauss integrals, Proc. Natl. Acad. Sci, pp.119-124, 2003.
DOI : 10.1073/pnas.2636460100

T. Harder, M. Borg, W. Boomsma, P. Røgen, and T. Hamelryck, Fast large-scale clustering of protein structures using Gauss integrals, Bioinformatics, vol.28, issue.4, pp.510-515, 2012.
DOI : 10.1093/bioinformatics/btr692

Y. Zhang and J. Skolnick, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Research, vol.33, issue.7, pp.2302-2309, 2005.
DOI : 10.1093/nar/gki524

R. H. Lathrop, The protein threading problem with sequence amino acid interaction preferences is NP-complete, "Protein Engineering, Design and Selection", vol.7, issue.9, pp.1059-1068, 1994.
DOI : 10.1093/protein/7.9.1059

K. Horadam and M. Nyblom, Distances between sets based on set commonality, Discrete Applied Mathematics, vol.167, pp.310-314, 2014.
DOI : 10.1016/j.dam.2013.10.037

N. S. Altman, An introduction to kernel and nearest-neighbor nonparametric regression, Am. Stat, vol.46, pp.175-185, 1992.

N. Malod-dognin, J. Nicolas, M. Temerinac-ott, and M. Reisert, SHREC'10 Track: Protein Model Classification; The Eurographics Association, 2010.

G. Csaba, F. Birzele, and R. Zimmer, Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis, BMC Structural Biology, vol.9, issue.1, p.23, 2009.
DOI : 10.1186/1472-6807-9-23

I. Wohlers, F. S. Domingues, and G. W. Klau, Towards optimal alignment of protein structure distance matrices, Bioinformatics, vol.26, issue.18, pp.2273-2280, 2010.
DOI : 10.1093/bioinformatics/btq420

S. Wang, J. Ma, J. Peng, and J. Xu, Protein structure alignment beyond spatial proximity. Sci. Rep. 2013, 3, 1448. c 2015 by the authors This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license