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

C. Berbalk, C. S. Schwaiger, and P. Lackner, Accuracy analysis of multiple structure alignments, Protein Science, vol.40, issue.10, pp.2027-2035, 2009.
DOI : 10.1002/pro.213

G. Chapuis, M. L. Boudic-jamin, R. Andonov, H. Djidjev, and D. Lavenier, Parallel Seed-Based Approach to Protein Structure Similarity Detection, Lecture Notes in Computer Science, vol.8385, issue.2, pp.278-287, 2013.
DOI : 10.1007/978-3-642-55195-6_26

URL : https://hal.archives-ouvertes.fr/hal-00881507

L. Dagum and R. Menon, OpenMP: an industry standard API for shared-memory programming, IEEE Computational Science and Engineering, vol.5, issue.1, pp.46-55, 1998.
DOI : 10.1109/99.660313

J. Gibrat, T. Madej, H. Stephen, and . Bryant, Surprising similarities in structure comparison, Current Opinion in Structural Biology, vol.6, issue.3, pp.377-385, 1996.
DOI : 10.1016/S0959-440X(96)80058-3

W. Gropp, L. Ewing, A. Lusk, and . Skjellum, Using MPI: Portable Parallel Programming with the Message Passing Interface, 1999.

L. Holm and C. Sander, Protein Structure Comparison by Alignment of Distance Matrices, Journal of Molecular Biology, vol.233, issue.1, pp.123-138, 1993.
DOI : 10.1006/jmbi.1993.1489

L. Holm and C. Sander, Searching protein structure databases has come of age, Proteins: Structure, Function, and Genetics, vol.18, issue.3, pp.165-173, 1994.
DOI : 10.1002/prot.340190302

G. Karypis and V. Kumar, A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs, SIAM Journal on Scientific Computing, vol.20, issue.1, pp.359-392, 1998.
DOI : 10.1137/S1064827595287997

P. Koehl, Protein structure similarities, Current Opinion in Structural Biology, vol.11, issue.3, pp.348-353, 2001.
DOI : 10.1016/S0959-440X(00)00214-1

R. Kolodny, P. Koehl, and M. Levitt, Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures, Journal of Molecular Biology, vol.346, issue.4, pp.1173-1188, 2005.
DOI : 10.1016/j.jmb.2004.12.032

R. Kolodny and N. Linial, From The Cover: Approximate protein structural alignment in polynomial time, Proceedings of the National Academy of Sciences, vol.101, issue.33, pp.12201-12206, 2004.
DOI : 10.1073/pnas.0404383101

J. Konc and D. Jane?i?, ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment, Bioinformatics, vol.26, issue.9, pp.1160-1168, 2010.
DOI : 10.1093/bioinformatics/btq100

P. Lackner, W. A. Koppensteiner, M. J. Sippl, and F. S. Domingues, ProSup: a refined tool for protein structure alignment, Protein Engineering Design and Selection, vol.13, issue.11, pp.745-752, 2000.
DOI : 10.1093/protein/13.11.745

T. Lai and S. Sahni, Anomalies in parallel branch-and-bound algorithms, Communications of the ACM, vol.27, issue.6, pp.594-602, 1984.
DOI : 10.1145/358080.358103

R. 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

P. Liu, K. Dimitris, . Agrafiotis, L. Douglas, and . Theobald, Fast determination of the optimal rotational matrix for macromolecular superpositions, Journal of Computational Chemistry, vol.450, issue.Suppl 2, pp.311561-1563, 2010.
DOI : 10.1002/jcc.21439

W. Liu, A. Srivastava, and J. Zhang, A Mathematical Framework for Protein Structure Comparison, PLoS Computational Biology, vol.6, issue.2, p.1001075, 2011.
DOI : 10.1371/journal.pcbi.1001075.t002

N. Malod-dognin, R. Andonov, and N. Yanev, Maximum Cliques in Protein Structure Comparison, Experimental Algorithms, pp.106-117, 2010.
DOI : 10.1007/978-3-642-13193-6_10

URL : https://hal.archives-ouvertes.fr/inria-00536700

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, 2014.
DOI : 10.1093/bioinformatics/btu020

S. Minami, K. Sawada, and G. Chikenji, MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C?? only models, Alternative alignments, and Non-sequential alignments, BMC Bioinformatics, vol.14, issue.1, pp.1-22, 2013.
DOI : 10.1016/j.jmb.2005.12.084

B. Kevin, . Murray, R. William, J. M. Taylor, and . Thornton, Toward the detection and validation of repeats in protein structure, Proteins, vol.57, issue.2, pp.365-80, 2004.

R. Parra, R. Espada, E. Ignacio, . Sánchez, J. Manfred et al., Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space, The Journal of Physical Chemistry B, vol.117, issue.42, pp.12887-97, 2013.
DOI : 10.1021/jp402105j

S. Salem, J. Mohammed, C. Zaki, and . Bystroff, FlexSnap: flexible non-sequential protein structure alignment. Algorithms for molecular biology, p.12, 2010.

T. Schank and D. Wagner, Finding, Counting and Listing All Triangles in Large Graphs, an Experimental Study, Experimental and Efficient Algorithms, pp.606-609, 2005.
DOI : 10.1007/11427186_54

S. Schmitt, D. Kuhn, and G. Klebe, A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology, Journal of Molecular Biology, vol.323, issue.2, pp.387-406, 2002.
DOI : 10.1016/S0022-2836(02)00811-2

I. Shindyalov and P. Bourne, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engineering Design and Selection, vol.11, issue.9, pp.739-747, 1998.
DOI : 10.1093/protein/11.9.739

D. M. Strickland, E. Barnes, and J. S. Sokol, Optimal Protein Structure Alignment Using Maximum Cliques, Operations Research, vol.53, issue.3, pp.389-402, 2005.
DOI : 10.1287/opre.1040.0189

S. Subbiah, D. V. Laurents, and M. Levitt, Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core, Current Biology, vol.3, issue.3, pp.141-148, 1993.
DOI : 10.1016/0960-9822(93)90255-M

I. Wohlers, R. Andonov, W. Gunnar, and . Klau, DALIX: Optimal DALI Protein Structure Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.1, pp.26-36, 2013.
DOI : 10.1109/TCBB.2012.143

I. Wohlers, L. Petzold, F. Domingues, and G. Klau, PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation, BMC Bioinformatics, vol.10, issue.Suppl 13, p.2, 2009.
DOI : 10.1186/1471-2105-10-S13-P2

A. Zemla, LGA: a method for finding 3D similarities in protein structures, Nucleic Acids Research, vol.31, issue.13, pp.3370-3374, 2003.
DOI : 10.1093/nar/gkg571

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

Y. Zhang and J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.4, pp.702-710, 2004.
DOI : 10.1002/prot.20264