S. Akanuma, T. Kigawa, and S. Yokoyama, Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set, Proceedings of the National Academy of Sciences, vol.49, issue.1, pp.13549-53, 2002.
DOI : 10.1007/PL00006522

R. Aurora, T. Creamer, R. Srinivasan, and G. Rose, Local Interactions in Protein Folding: Lessons from the ??-Helix, Journal of Biological Chemistry, vol.272, issue.3, pp.1413-1419, 1997.
DOI : 10.1074/jbc.272.3.1413

C. Benros, Analyse et prédiction des structures tridimensionnelles locales des protéines, p.212, 2005.

C. Benros, A. De-brevern, C. Etchebest, and S. Hazout, Assessing a novel approach for predicting local 3D protein structures from sequence, Proteins: Structure, Function, and Bioinformatics, vol.30, issue.23, pp.865-880, 2006.
DOI : 10.1002/prot.20815

URL : https://hal.archives-ouvertes.fr/inserm-00133180

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat et al., The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-277, 2000.
DOI : 10.1093/nar/28.1.235

L. Bradley, P. Thumfort, and M. Hecht, <i>De novo</i> Proteins From Binary-Patterned Combinatorial Libraries, Methods Mol Biol, vol.340, pp.53-69, 2006.
DOI : 10.1385/1-59745-116-9:53

L. Bradley, Y. Wei, P. Thumfort, C. Wurth, and M. Hecht, Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids, Methods Mol Biol, vol.352, pp.155-66, 2007.
DOI : 10.1385/1-59745-187-8:155

B. Brown and R. Sauer, Tolerance of Arc repressor to multiple-alanine substitutions, Proceedings of the National Academy of Sciences, vol.24, issue.2, pp.1983-1991, 1999.
DOI : 10.1038/nsb0295-122

C. Buhot, A. Chenal, A. Sanson, S. Pouvelle-moratille, M. Gelb et al., Alteration of the tertiary structure of the major bee venom allergen Api m 1 by multiple mutations is concomitant with low IgE reactivity, Protein Science, vol.38, issue.11, pp.2970-2978, 2004.
DOI : 10.1110/ps.04885404

A. Camproux, R. Gautier, and P. Tuffery, A Hidden Markov Model Derived Structural Alphabet for Proteins, Journal of Molecular Biology, vol.339, issue.3, pp.591-605, 2004.
DOI : 10.1016/j.jmb.2004.04.005

A. Camproux, P. Tuffery, J. Chevrolat, J. Boisvieux, and S. Hazout, Hidden Markov model approach for identifying the modular framework of the protein backbone, Protein Engineering Design and Selection, vol.12, issue.12, pp.1063-73, 1999.
DOI : 10.1093/protein/12.12.1063

H. Chan, Folding alphabets, Nature Structural Biology, vol.6, issue.11, pp.994-1000, 1999.
DOI : 10.1038/14876

H. Chan and K. Dill, Origins of structure in globular proteins., Proceedings of the National Academy of Sciences, vol.87, issue.16, pp.6388-92, 1990.
DOI : 10.1073/pnas.87.16.6388

C. Chothia, M. Levitt, and D. Richardson, Structure of proteins: packing of alpha-helices and pleated sheets., Proceedings of the National Academy of Sciences, vol.74, issue.10, pp.4130-4134, 1977.
DOI : 10.1073/pnas.74.10.4130

M. Cieplak, N. Holter, A. Maritan, and J. Banavar, Amino acid classes and the protein folding problem, The Journal of Chemical Physics, vol.114, issue.3, pp.1420-1423, 2001.
DOI : 10.1063/1.1333025

N. Clarke, Sequence ???minimization???: exploring the sequence landscape with simplified sequences, Current Opinion in Biotechnology, vol.6, issue.4, pp.467-72, 1995.
DOI : 10.1016/0958-1669(95)80077-8

N. Colloc-'h, C. Etchebest, E. Thoreau, B. Henrissat, and J. Mornon, Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment, "Protein Engineering, Design and Selection", vol.6, issue.4, pp.377-82, 1993.
DOI : 10.1093/protein/6.4.377

URL : https://hal.archives-ouvertes.fr/hal-00310605

A. De-brevern, New assessment of Protein Blocks, In Silico Biology, vol.5, pp.283-289, 2005.

A. De-brevern, C. Benros, R. Gautier, H. Valadie, S. Hazout et al., Local backbone structure prediction of proteins, In Silico Biol, vol.4, pp.381-387, 2004.
URL : https://hal.archives-ouvertes.fr/inserm-00132872

A. De-brevern, C. Etchebest, C. Benros, and S. Hazout, ???Pinning strategy???: a novel approach for predicting the backbone structure in terms of protein blocks from sequence, Journal of Biosciences, vol.289, issue.1, pp.51-70, 2007.
DOI : 10.1007/s12038-007-0006-3

A. De-brevern, C. Etchebest, and S. Hazout, Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins: Structure, Function, and Genetics, vol.7, issue.3, pp.271-87, 2000.
DOI : 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z

URL : https://hal.archives-ouvertes.fr/inserm-00132821

A. De-brevern and S. Hazout, 'Hybrid Protein Model' for optimally defining 3D protein structure fragments, Bioinformatics, vol.19, issue.3, pp.345-53, 2003.
DOI : 10.1093/bioinformatics/btf859

URL : https://hal.archives-ouvertes.fr/inserm-00133632

A. De-brevern, H. Valadie, S. Hazout, and C. Etchebest, Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship, Protein Science, vol.40, issue.(1/2), pp.2871-86, 2002.
DOI : 10.1110/ps.0220502

URL : https://hal.archives-ouvertes.fr/inserm-00143374

K. Dill, Theory for the folding and stability of globular proteins, Biochemistry, vol.24, issue.6, pp.1501-1510, 1985.
DOI : 10.1021/bi00327a032

K. Dill, S. Bromberg, K. Yue, K. Fiebig, D. Yee et al., Principles of protein folding - A perspective from simple exact models, Protein Science, vol.89, issue.2, pp.561-602, 1995.
DOI : 10.1002/pro.5560040401

N. Dokholyan, What is the protein design alphabet?, Proteins: Structure, Function, and Bioinformatics, vol.311, issue.4, pp.622-630, 2004.
DOI : 10.1002/prot.10633

N. Dokholyan, Studies of folding and misfolding using simplified models, Current Opinion in Structural Biology, vol.16, issue.1, pp.1-7, 2005.
DOI : 10.1016/j.sbi.2006.01.001

O. Dubreuil, M. Bossus, M. Graille, M. Bilous, A. Savatier et al., Fine Tuning of the Specificity of an Anti-progesterone Antibody by First and Second Sphere Residue Engineering, Journal of Biological Chemistry, vol.280, issue.26, pp.24880-24887, 2005.
DOI : 10.1074/jbc.M500048200

M. Dudev and C. Lim, Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites, BMC Bioinformatics, vol.8, issue.1, p.106, 2007.
DOI : 10.1186/1471-2105-8-106

J. Esteve and F. Falceto, A general clustering approach with application to the Miyazawa-Jernigan potentials for amino acids, Proteins: Structure, Function, and Bioinformatics, vol.88, issue.4, pp.999-1004, 2004.
DOI : 10.1002/prot.10570

J. Esteve and F. Falceto, Classification of amino acids induced by their associated matrices, Biophysical Chemistry, vol.115, issue.2-3, pp.177-80, 2005.
DOI : 10.1016/j.bpc.2004.12.023

C. Etchebest, C. Benros, S. Hazout, and A. De-brevern, A structural alphabet for local protein structures: Improved prediction methods, Proteins: Structure, Function, and Bioinformatics, vol.20, issue.4, pp.810-827, 2005.
DOI : 10.1002/prot.20458

URL : https://hal.archives-ouvertes.fr/inserm-00143564

K. Fan and W. Wang, What is the Minimum Number of Letters Required to Fold a Protein?, Journal of Molecular Biology, vol.328, issue.4, pp.921-927, 2003.
DOI : 10.1016/S0022-2836(03)00324-3

N. Fitzkee, P. Fleming, H. Gong, N. Panasik, J. Street et al., Are proteins made from a limited parts list?, Trends in Biochemical Sciences, vol.30, issue.2, pp.73-80, 2005.
DOI : 10.1016/j.tibs.2004.12.005

L. Fourrier, C. Benros, and A. De-brevern, Use of a structural alphabet for analysis of short loops connecting repetitive structures, BMC Bioinformatics, vol.5, issue.1, p.58, 2004.
DOI : 10.1186/1471-2105-5-58

URL : https://hal.archives-ouvertes.fr/inserm-00112104

N. Franks, A. Jenkins, E. Conti, W. Lieb, and P. Brick, Structural Basis for the Inhibition of Firefly Luciferase by a General Anesthetic, Biophysical Journal, vol.75, issue.5, pp.2205-2216, 1998.
DOI : 10.1016/S0006-3495(98)77664-7

C. Gaboriaud, V. Bissery, T. Benchetrit, and J. Mornon, Hydrophobic cluster analysis: An efficient new way to compare and analyse amino acid sequences, FEBS Letters, vol.112, issue.1, pp.149-155, 1987.
DOI : 10.1016/0014-5793(87)80439-8

M. Hecht, A. Das, A. Go, L. Bradley, and Y. Wei, De novo proteins from designed combinatorial libraries, Protein Science, vol.15, issue.7, pp.1711-1734, 2004.
DOI : 10.1110/ps.04690804

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279937

S. Henikoff and J. Henikoff, Amino acid substitution matrices from protein blocks., Proceedings of the National Academy of Sciences, vol.89, issue.22, pp.10915-10924, 1992.
DOI : 10.1073/pnas.89.22.10915

R. Ihaka and R. Gentleman, R: a language for data analysis and graphics, J Comput Graph Stat, vol.5, pp.299-314, 1996.

Y. Ikenaka, H. Nanba, K. Yajima, Y. Yamada, M. Takano et al., -Amino Acid Amidohydrolase on Amino Acid Substitutions, Bioscience, Biotechnology, and Biochemistry, vol.62, issue.9, pp.1668-71, 1998.
DOI : 10.1271/bbb.62.1668

URL : https://hal.archives-ouvertes.fr/hal-00078132

Y. Ikenaka, H. Nanba, Y. Yamada, K. Yajima, M. Takano et al., -Amino acid Amidohydrolase from Thermotolerant Soil Bacteria, Bioscience, Biotechnology, and Biochemistry, vol.62, issue.5, pp.882-888, 1998.
DOI : 10.1271/bbb.62.882

URL : https://hal.archives-ouvertes.fr/hal-00078132

S. Kamtekar, J. Schiffer, H. Xiong, J. Babik, and M. Hecht, Protein design by binary patterning of polar and nonpolar amino acids, Science, vol.262, issue.5140, pp.1680-1685, 1993.
DOI : 10.1126/science.8259512

R. Karchin, Evaluating local structure alphabets for protein structure prediction, p.301, 2003.

R. Karchin, M. Cline, Y. Mandel-gutfreund, and K. Karplus, Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry, Proteins: Structure, Function, and Bioinformatics, vol.323, issue.1/2, pp.504-518, 2003.
DOI : 10.1002/prot.10369

Y. Kim, A. Berry, D. Spencer, and W. Stites, Comparing the effect on protein stability of methionine oxidation versus mutagenesis: steps toward engineering oxidative resistance in proteins, Protein Engineering Design and Selection, vol.14, issue.5, pp.343-350, 2001.
DOI : 10.1093/protein/14.5.343

B. Kuhlman and D. Baker, Exploring folding free energy landscapes using computational protein design, Current Opinion in Structural Biology, vol.14, issue.1, pp.89-95, 2004.
DOI : 10.1016/j.sbi.2004.01.002

S. Kumar and M. Bansal, Geometrical and Sequence Characteristics of ??-Helices in Globular Proteins, Biophysical Journal, vol.75, issue.4, pp.1935-1979, 1998.
DOI : 10.1016/S0006-3495(98)77634-9

G. Law, O. Gandelman, L. Tisi, C. Lowe, and J. Murray, luciferase improves thermostability and pH-tolerance, Biochemical Journal, vol.397, issue.2, pp.305-317, 2006.
DOI : 10.1042/BJ20051847

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513288

T. Li, K. Fan, J. Wang, and W. Wang, Reduction of protein sequence complexity by residue grouping, Protein Engineering Design and Selection, vol.16, issue.5, pp.323-353, 2003.
DOI : 10.1093/protein/gzg044

X. Liu, L. Zhang, S. Guan, and W. Zheng, Distances and classification of amino acids for different protein secondary structures, Physical Review E, vol.67, issue.5, p.51927, 2003.
DOI : 10.1103/PhysRevE.67.051927

F. Melo and M. Marti-renom, Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets, Proteins: Structure, Function, and Bioinformatics, vol.48, issue.4, pp.986-95, 2006.
DOI : 10.1002/prot.20881

S. Miyazawa and R. Jernigan, A new substitution matrix for protein sequence searches based on contact frequencies in protein structures, "Protein Engineering, Design and Selection", vol.6, issue.3, pp.267-78, 1993.
DOI : 10.1093/protein/6.3.267

L. Murphy, A. Wallqvist, and R. Levy, Simplified amino acid alphabets for protein fold recognition and implications for folding, Protein Engineering Design and Selection, vol.13, issue.3, pp.149-52, 2000.
DOI : 10.1093/protein/13.3.149

H. Nanba, Y. Ikenaka, Y. Yamada, K. Yajima, M. Takano et al., -Amino Acid Amidohydrolase, Cloning of the Gene for this Enzyme, and Properties of the Enzyme, Bioscience, Biotechnology, and Biochemistry, vol.62, issue.5, pp.875-81, 1998.
DOI : 10.1271/bbb.62.875

URL : https://hal.archives-ouvertes.fr/jpa-00222503

T. Noguchi and Y. Akiyama, PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003, Nucleic Acids Research, vol.31, issue.1, pp.492-495, 2003.
DOI : 10.1093/nar/gkg022

T. Noguchi, H. Matsuda, and Y. Akiyama, PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), Nucleic Acids Research, vol.29, issue.1, pp.219-239, 2001.
DOI : 10.1093/nar/29.1.219

K. Oh, S. Nam, and H. Kim, Improvement of Oxidative and Thermostability of N-Carbamyl-D-Amino Acid Amidohydrolase by Directed Evolution, Protein Engineering Design and Selection, vol.15, issue.8, pp.689-95, 2002.
DOI : 10.1093/protein/15.8.689

K. Plaxco, D. Riddle, V. Grantcharova, and D. Baker, Simplified proteins: minimalist solutions to the ???protein folding problem???, Current Opinion in Structural Biology, vol.8, issue.1, pp.80-85, 1998.
DOI : 10.1016/S0959-440X(98)80013-4

L. Regan and W. Degrado, Characterization of a helical protein designed from first principles, Science, vol.241, issue.4868, pp.976-984, 1988.
DOI : 10.1126/science.3043666

D. Riddle, J. Santiago, S. Bray-hall, N. Doshi, V. Grantcharova et al., Functional rapidly folding proteins from simplified amino acid sequences, Nature Structural Biology, vol.50, issue.10, pp.805-814, 1997.
DOI : 10.1016/S0263-7855(98)80030-1

S. Rogov and A. Nekrasov, A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences, Protein Engineering Design and Selection, vol.14, issue.7, pp.459-63, 2001.
DOI : 10.1093/protein/14.7.459

A. Sali, E. Shakhnovich, and M. Karplus, Kinetics of Protein Folding, Journal of Molecular Biology, vol.235, issue.5, pp.1614-1650, 1994.
DOI : 10.1006/jmbi.1994.1110

J. Sammon and J. W. , A Nonlinear Mapping for Data Structure Analysis, IEEE Transactions on Computers, vol.18, issue.5, pp.401-409, 1969.
DOI : 10.1109/T-C.1969.222678

O. Sander, I. Sommer, and T. Lengauer, Local protein structure prediction using discriminative models, BMC Bioinformatics, vol.7, issue.1, p.14, 2006.
DOI : 10.1186/1471-2105-7-14

R. Smith and T. Smith, Automatic generation of primary sequence patterns from sets of related protein sequences., Proceedings of the National Academy of Sciences, vol.87, issue.1, pp.118-140, 1990.
DOI : 10.1073/pnas.87.1.118

A. Solis and S. Rackovsky, Optimized representations and maximal information in proteins, Proteins: Structure, Function, and Genetics, vol.213, issue.2, pp.149-64, 2000.
DOI : 10.1002/(SICI)1097-0134(20000201)38:2<149::AID-PROT4>3.0.CO;2-#

M. Tyagi, New perspectives for protein structure analysis and mining using sequences of a structural alphabet, p.215, 2006.

M. Tyagi, V. Gowri, N. Srinivasan, A. De-brevern, and B. Offmann, A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications, Proteins: Structure, Function, and Bioinformatics, vol.272, issue.1, pp.32-41, 2006.
DOI : 10.1002/prot.21087

URL : https://hal.archives-ouvertes.fr/inserm-00133760

M. Tyagi, P. Sharma, C. Swamy, F. Cadet, N. Srinivasan et al., Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet, Nucleic Acids Research, vol.34, issue.Web Server, pp.119-142, 2006.
DOI : 10.1093/nar/gkl199

URL : https://hal.archives-ouvertes.fr/inserm-00133751

R. Unger, D. Harel, S. Wherland, and J. Sussman, A 3D building blocks approach to analyzing and predicting structure of proteins, Proteins: Structure, Function, and Genetics, vol.5, issue.4, pp.355-73, 1989.
DOI : 10.1002/prot.340050410

J. Wang and W. Wang, A computational approach to simplifying the protein folding alphabet, Nature Structural Biology, vol.6, issue.11, pp.1033-1041, 1999.
DOI : 10.1038/14918

W. Wang, W. Hsu, F. Chien, and C. Chen, Crystal structure and site-directed mutagenesis studies of N-carbamoyl-d-amino-acid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft11Edited by R. Huber, Journal of Molecular Biology, vol.306, issue.2, pp.251-61, 2001.
DOI : 10.1006/jmbi.2000.4380

Y. Wei, S. Kim, D. Fela, J. Baum, and M. Hecht, Solution structure of a de novo protein from a designed combinatorial library, Proceedings of the National Academy of Sciences, vol.50, issue.3, pp.13270-13273, 2003.
DOI : 10.1002/prot.10286

J. Wrabl and N. Grishin, Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization, Proteins: Structure, Function, and Bioinformatics, vol.65, issue.Suppl 6, pp.523-557, 2005.
DOI : 10.1002/prot.20648

W. Xu and D. Miranker, A metric model of amino acid substitution, Bioinformatics, vol.20, issue.8, pp.1214-1235, 2004.
DOI : 10.1093/bioinformatics/bth065

K. Yue, K. Fiebig, P. Thomas, H. Chan, E. Shakhnovich et al., A test of lattice protein folding algorithms., Proceedings of the National Academy of Sciences, vol.92, issue.1, pp.325-334, 1995.
DOI : 10.1073/pnas.92.1.325