A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis, Nature, vol.178, issue.4610, pp.662-666, 1958. ,
DOI : 10.1002/hlca.19490320118
Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.235-240, 1951. ,
DOI : 10.1073/pnas.37.5.235
The discovery of the ??-helix and ??-sheet, the principal structural features of proteins, Proceedings of the National Academy of Sciences, vol.47, issue.4, pp.11207-11210, 2003. ,
DOI : 10.1016/S0022-2836(63)80023-6
The Pleated Sheet, A New Layer Configuration of Polypeptide Chains, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.251-256, 1951. ,
DOI : 10.1073/pnas.37.5.251
TWO HYDROGEN-BONDED SPIRAL CONFIGURATIONS OF THE POLYPEPTIDE CHAIN, Journal of the American Chemical Society, vol.72, issue.11, p.53, 1950. ,
DOI : 10.1021/ja01167a545
Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the ??-helix, Protein Science, vol.285, issue.11, pp.2508-2522, 2003. ,
DOI : 10.1110/ps.03235203
??-Breakers: An aperiodic secondary structure, Journal of Molecular Biology, vol.221, issue.2, pp.603-613, 1991. ,
DOI : 10.1016/0022-2836(91)80075-6
Protein Structure: Born to be beta, Current Biology, vol.4, issue.7, pp.656-658, 1994. ,
DOI : 10.1016/S0960-9822(00)00147-0
Natural ??-sheet proteins use negative design to avoid edge-to-edge aggregation, Proceedings of the National Academy of Sciences, vol.268, issue.4, pp.2754-2759, 2002. ,
DOI : 10.1006/jmbi.1994.1691
Handedness of crossover connections in beta sheets., Proceedings of the National Academy of Sciences, vol.73, issue.8, pp.2619-2623, 1976. ,
DOI : 10.1073/pnas.73.8.2619
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
Helix to helix packing in proteins, Journal of Molecular Biology, vol.145, issue.1, pp.215-250, 1981. ,
DOI : 10.1016/0022-2836(81)90341-7
Structure of coiled ??-??-hairpins and ??-??-corners, FEBS Letters, vol.224, issue.2, pp.288-292, 1991. ,
DOI : 10.1016/0014-5793(91)80706-9
Rules for alpha-helix termination by glycine, Science, vol.264, issue.5162, pp.1126-1130, 1994. ,
DOI : 10.1126/science.8178170
Determinants of strand register in antiparallel ??-sheets of proteins, Protein Science, vol.22, issue.11, pp.2287-2300, 1998. ,
DOI : 10.1002/pro.5560071106
Helix capping, Protein Science, vol.31, issue.1, pp.21-38, 1998. ,
DOI : 10.1002/pro.5560070103
Singular points of protein ??-sheets, Protein Science, vol.3, issue.11, pp.2324-2330, 1998. ,
DOI : 10.1002/pro.5560071109
Hydrogen Bonded Helical Configurations of the Polypeptide Chain, Proceedings of the National Academy of Sciences, vol.39, issue.6, pp.470-478, 1953. ,
DOI : 10.1073/pnas.39.6.470
Novel protein structural motifs containing two-turn and longer 310-helices, Protein Engineering Design and Selection, vol.12, issue.10, pp.811-814, 1999. ,
DOI : 10.1093/protein/12.10.811
Variants of 310-helices in proteins, Proteins: Structure, Function, and Genetics, vol.32, issue.3, pp.571-579, 2002. ,
DOI : 10.1002/prot.10184
THE ?? HELIX???A HYDROGEN BONDED CONFIGURATION OF THE POLYPEPTIDE CHAIN, Journal of the American Chemical Society, vol.74, issue.22, p.5806, 1952. ,
DOI : 10.1021/ja01142a539
Generalized Mathematical Relationships for Polypeptide Chain Helices: The Coordinates of the II Helix, Proceedings of the National Academy of Sciences, vol.39, issue.8, pp.785-801, 1953. ,
DOI : 10.1073/pnas.39.8.785
The ??-helix translates structure into function, Protein Science, vol.21, issue.1, pp.201-206, 2000. ,
DOI : 10.1110/ps.9.1.201
Occurrence, conformational features and amino acid propensities for the ??-helix, Protein Engineering Design and Selection, vol.15, issue.5, pp.353-358, 2002. ,
DOI : 10.1093/protein/15.5.353
??-Helix Preference in Unsolvated Peptides, Journal of the American Chemical Society, vol.126, issue.9, pp.2777-2784, 2004. ,
DOI : 10.1021/ja0381353
-, and ??-helix in helix???coil transitions, Protein Science, vol.31, issue.102, pp.1145-1157, 2003. ,
DOI : 10.1110/ps.0240103
Structural and Functional Characterization of ?? Bulges and Other Short Intrahelical Deformations, Structure, vol.12, issue.1, pp.133-144, 2004. ,
DOI : 10.1016/j.str.2003.12.001
The Structure of Fibrous Proteins of the Collagen- HAL author manuscript inserm-00134564, 1951. ,
Structure of Poly-L-Proline, Nature, vol.7, issue.4480, pp.501-503, 1955. ,
DOI : 10.1021/ja01176a005
Left-handed Polyproline II Helices Commonly Occur in Globular Proteins, Journal of Molecular Biology, vol.229, issue.2, pp.472-493, 1993. ,
DOI : 10.1006/jmbi.1993.1047
A survey of left-handed polyproline II helices, Protein Science, vol.117, issue.3, pp.587-595, 1999. ,
DOI : 10.1110/ps.8.3.587
Left-handed polyproline II helix formation is (very) locally driven, Proteins: Structure, Function, and Genetics, vol.24, issue.2, pp.218-226, 1998. ,
DOI : 10.1002/(SICI)1097-0134(19981101)33:2<218::AID-PROT6>3.0.CO;2-E
Determinants of the polyproline II helix from modeling studies, Adv Protein Chem, vol.62, pp.263-282, 2002. ,
DOI : 10.1016/S0065-3233(02)62010-8
Stranded in isolation: structural role of isolated extended strands in proteins, Protein Engineering Design and Selection, vol.16, issue.5, pp.331-339, 2003. ,
DOI : 10.1093/protein/gzg046
Orthogonal ???? motifs in proteins, Journal of Molecular Biology, vol.223, issue.4, pp.845-851, 1992. ,
DOI : 10.1016/0022-2836(92)90246-G
The beta bulge: a common small unit of nonrepetitive protein structure., Proceedings of the National Academy of Sciences, vol.75, issue.6, pp.2574-2578, 1978. ,
DOI : 10.1073/pnas.75.6.2574
Identification, classification, and analysis of beta-bulges in proteins, Protein Science, vol.170, issue.10, pp.1574-1590, 1993. ,
DOI : 10.1002/pro.5560021004
An irregular beta-bulge common to a group of bacterial RNases is an important determinant of stability and function, 1999. ,
Conformation of Polypeptides and Proteins, Protein Chem, vol.23, p.283, 1968. ,
DOI : 10.1016/S0065-3233(08)60402-7
Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units, Biopolymers, vol.1, issue.10, pp.1425-1436, 1968. ,
DOI : 10.1002/bip.1968.360061006
URL : http://deepblue.lib.umich.edu/bitstream/2027.42/33067/1/0000453.pdf
The beta bulge: a common small unit of nonrepetitive protein structure., Proceedings of the National Academy of Sciences, vol.75, issue.6, pp.2574-2578, 1978. ,
DOI : 10.1073/pnas.75.6.2574
The ?? Turn, a Possible Folded Conformation of the Polypeptide Chain. Comparison with the ?? Turn, Macromolecules, vol.5, issue.6, pp.755-758, 1972. ,
DOI : 10.1021/ma60030a017
The ?? Turn. Evidence for a New Folded Conformation in Proteins, Macromolecules, vol.5, issue.6, pp.818-819, 1972. ,
DOI : 10.1021/ma60030a031
Recurring loop motif in proteins that occurs in right-handed and left-handed forms, Journal of Molecular Biology, vol.199, issue.3, pp.503-511, 1988. ,
DOI : 10.1016/0022-2836(88)90621-3
Turns in Peptides and Proteins, Adv. Prot. Chem, vol.37, pp.1-109, 1985. ,
DOI : 10.1016/S0065-3233(08)60063-7
Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding, Proceedings of the National Academy of Sciences, vol.68, issue.9, pp.2293-2297, 1971. ,
DOI : 10.1073/pnas.68.9.2293
Protein folding, Journal of the American Chemical Society, vol.94, issue.11, pp.4009-4012, 1972. ,
DOI : 10.1021/ja00766a060
Chain reversals in proteins, Biochimica et Biophysica Acta (BBA) - Protein Structure, vol.303, issue.2, pp.211-229, 1973. ,
DOI : 10.1016/0005-2795(73)90350-4
??-turns in proteins, Journal of Molecular Biology, vol.115, issue.2, pp.135-175, 1977. ,
DOI : 10.1016/0022-2836(77)90094-8
A new algorithm for finding the peptide chain turns in a globular protein, Journal of Molecular Biology, vol.113, issue.1, pp.153-164, 1977. ,
DOI : 10.1016/0022-2836(77)90046-8
The number of turns in globular proteins, Nature, vol.155, issue.5622, pp.769-770, 1977. ,
DOI : 10.1038/260729a0
Influence of local interactions on protein structure. I. Conformational energy studies ofN-acetyl-N?-methylamides of pro-X and X-pro dipeptides, Biopolymers, vol.97, issue.4, pp.811-843, 1977. ,
DOI : 10.1002/bip.1977.360160408
The Anatomy and Taxonomy of Protein Structure, Adv Protein Chem, vol.34, pp.167-339, 1981. ,
DOI : 10.1016/S0065-3233(08)60520-3
Analysis and prediction of the different types of ?turn in proteins, J Mol Biol, vol.5, pp.221-232, 1988. ,
PROMOTIF-A program to identify and analyze structural motifs in proteins, Protein Science, vol.3, issue.2, pp.212-220, 1996. ,
DOI : 10.1002/pro.5560050204
??-turn topography, Tetrahedron, vol.49, issue.17, pp.3467-3478 ,
DOI : 10.1016/S0040-4020(01)90207-8
Characterization of a novel type VII ??-turn conformation for a bio-active tetrapeptide rigin, European Journal of Biochemistry, vol.44, issue.5, pp.1455-1463, 2000. ,
DOI : 10.1046/j.1432-1327.2000.01144.x
Prediction of Tight Turns and Their Types in Proteins, Analytical Biochemistry, vol.286, issue.1, pp.1-16, 2000. ,
DOI : 10.1006/abio.2000.4757
Discovering protein secondary structures: Classification and description of isolated ??-turns, Biopolymers, vol.221, issue.6, pp.705-721, 1996. ,
DOI : 10.1002/(SICI)1097-0282(199606)38:6<705::AID-BIP3>3.0.CO;2-V
Prediction of ??-turns in proteins using PSI-BLAST profiles and secondary structure information, Proteins: Structure, Function, and Bioinformatics, vol.114, issue.1, pp.83-90, 2004. ,
DOI : 10.1002/prot.10569
One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins, Journal of Molecular Biology, vol.204, issue.3, pp.777-782, 1988. ,
DOI : 10.1016/0022-2836(88)90368-3
?-turns in proteins and peptides: HAL author manuscript inserm-00134564, 1996. ,
beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials, J Biosci, vol.25, pp.143-156, 2000. ,
Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins, Journal of Peptide Research, vol.16, issue.4, pp.250-263, 2000. ,
DOI : 10.1107/S0907444998009378
Combinations of turns in proteins, Journal of Peptide Research, vol.62, issue.4, pp.167-174, 2003. ,
DOI : 10.1034/j.1399-3011.2003.00086.x
Loops in globular proteins: a novel category of secondary structure, Science, vol.234, issue.4778, pp.849-855, 1986. ,
DOI : 10.1126/science.3775366
Omega loops: nonregular secondary structures significant in protein function and stability, FASEB J, vol.9, pp.708-717, 1995. ,
The nature of the turn in omega loops of proteins, Proteins: Structure, Function, and Bioinformatics, vol.99, issue.4, pp.606-616, 2003. ,
DOI : 10.1002/prot.10376
Deletions and replacements of omega loops in yeast iso-1-cytochromec, Proteins: Structure, Function, and Genetics, vol.237, issue.4, pp.372-381, 1989. ,
DOI : 10.1002/prot.340060404
Cooperative Omega Loops in Cytochrome c: Role in Folding and Function, Journal of Molecular Biology, vol.331, issue.1, pp.29-36, 2003. ,
DOI : 10.1016/S0022-2836(03)00697-1
??-Hairpin families in globular proteins, Nature, vol.19, issue.6024, pp.170-174, 1985. ,
DOI : 10.1038/316170a0
-hairpins in proteins, Biochemical Journal, vol.240, issue.1, pp.289-292, 1986. ,
DOI : 10.1042/bj2400289
URL : https://hal.archives-ouvertes.fr/hal-01299213
Conformation of beta-hairpins in HAL author manuscript inserm-00134564, 1989. ,
[5] Conformation of ?? hairpins in protein structures: Classification and diversity in homologous structures, Methods Enzymol, vol.202, pp.59-82, 1991. ,
DOI : 10.1016/0076-6879(91)02007-V
Accommodating Sequence Changes in ??-Hairpins in Proteins, Journal of Molecular Biology, vol.229, issue.2, pp.428-447, 1993. ,
DOI : 10.1006/jmbi.1993.1044
Beta-hairpins in proteins revisited: lessons for de novo design, Protein Engineering Design and Selection, vol.10, issue.10, pp.1131-1141, 1997. ,
DOI : 10.1093/protein/10.10.1131
Turn stability in ??-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns, Protein Science, vol.3, issue.2, pp.237-247, 2003. ,
DOI : 10.1110/ps.0228603
Identification of a Key Structural Element for Protein Folding Within ??-Hairpin Turns, Journal of Molecular Biology, vol.328, issue.4, pp.951-961, 2003. ,
DOI : 10.1016/S0022-2836(03)00321-8
A novel super-secondary structure of proteins and the relation between the structure and the amino acid sequence, FEBS Letters, vol.10, issue.1, pp.33-38, 1984. ,
DOI : 10.1016/0014-5793(84)80039-3
A helix-turn-strand structural motif common in ??-?? proteins, Proteins: Structure, Function, and Genetics, vol.85, issue.4, pp.334-340, 1990. ,
DOI : 10.1002/prot.340080407
Structural evidence for gene duplication in the evolution of the acid proteases, Nature, vol.248, issue.5646, pp.618-622, 1978. ,
DOI : 10.1038/267808a0
Automatic Classification and Analysis of ????-Turn Motifs in Proteins, Journal of Molecular Biology, vol.255, issue.1, pp.235-253, 1996. ,
DOI : 10.1006/jmbi.1996.0020
Typical interaction patterns in alphabeta and betaalpha turn motifs, Protein Engineering Design and Selection, vol.11, issue.7, pp.505-522, 1998. ,
DOI : 10.1093/protein/11.7.505
Structural classification of HAL author manuscript inserm-00134564, 1998. ,
A Global Taxonomy of Loops in Globular Proteins, Journal of Molecular Biology, vol.259, issue.4, pp.855-872, 1996. ,
DOI : 10.1006/jmbi.1996.0363
Linkers of secondary structures in proteins, Protein Science, vol.44, issue.12, pp.2538-2547, 1997. ,
DOI : 10.1002/pro.5560061206
Structural determinants of the conformations of medium-sized loops in proteins, Proteins: Structure, Function, and Genetics, vol.14, issue.4, pp.382-394, 1989. ,
DOI : 10.1002/prot.340060405
Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction, Protein Science, vol.6, issue.12, pp.2600-2616, 1996. ,
DOI : 10.1002/pro.5560051223
Protein loops on structurally similar scaffolds: Database and conformational analysis, Biopolymers, vol.229, issue.6, pp.481-495, 1999. ,
DOI : 10.1002/(SICI)1097-0282(199905)49:6<481::AID-BIP6>3.0.CO;2-V
Taxonomy and conformational analysis of loops in proteins, Journal of Molecular Biology, vol.224, issue.3, pp.685-699, 1992. ,
DOI : 10.1016/0022-2836(92)90553-V
Prediction of protein threedimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria, J Mol Biol, vol.267, pp.114-131, 1995. ,
Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling, Journal of Molecular Biology, vol.267, issue.2, pp.352-367, 1997. ,
DOI : 10.1006/jmbi.1996.0851
PDB-based protein loop prediction: parameters for selection and methods for optimization, Journal of Molecular Biology, vol.267, issue.4, pp.975-1001, 1997. ,
DOI : 10.1006/jmbi.1996.0857
New efficient statistical sequence- HAL author manuscript inserm-00134564, 1999. ,
Modeling of loops in protein structures, Protein Science, vol.14, issue.9, pp.1753-1773, 2000. ,
DOI : 10.1110/ps.9.9.1753
Comparison of systematic search and database methods for constructing segments of protein structure, "Protein Engineering, Design and Selection", vol.7, issue.8, pp.953-960, 1994. ,
DOI : 10.1093/protein/7.8.953
An automated classification of the structure of protein loops, Journal of Molecular Biology, vol.266, issue.4, pp.814-830, 1997. ,
DOI : 10.1006/jmbi.1996.0819
Loops In Proteins (LIP)--a comprehensive loop database for homology modelling, Protein Engineering Design and Selection, vol.16, issue.12, pp.979-985, 2003. ,
DOI : 10.1093/protein/gzg119
HELANAL: A Program to Characterize Helix Geometry in Proteins, Journal of Biomolecular Structure and Dynamics, vol.31, issue.5, pp.811-819, 2000. ,
DOI : 10.1107/S0021889891004399
Automatic identification of secondary structure in globular proteins, Journal of Molecular Biology, vol.114, issue.2, pp.181-293, 1977. ,
DOI : 10.1016/0022-2836(77)90207-8
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-2637, 1983. ,
DOI : 10.1002/bip.360221211
The protein data bank: A computer-based archival file for macromolecular structures, Journal of Molecular Biology, vol.112, issue.3, pp.535-540, 1977. ,
DOI : 10.1016/S0022-2836(77)80200-3
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Genetics, vol.206, issue.4, pp.566-579, 1995. ,
DOI : 10.1002/prot.340230412
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.9420
Continuum secondary HAL author manuscript inserm-00134564, 2002. ,
Secondary structure assignement in Structural, pp.341-364, 2002. ,
DSSPcont: continuous secondary structure assignments for proteins, Nucleic Acids Research, vol.31, issue.13, pp.3293-3295, 2003. ,
DOI : 10.1093/nar/gkg626
Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure, Proteins: Structure, Function, and Genetics, vol.72, issue.2, pp.71-84, 1988. ,
DOI : 10.1002/prot.340030202
Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis, Proteins: Structure, Function, and Genetics, vol.6, issue.1, pp.46-60, 1989. ,
DOI : 10.1002/prot.340060105
URL : https://hal.archives-ouvertes.fr/hal-00313453
PSEA: a new efficient assignment of secondary structure from C? trace of proteins, Comput Appl Biosci, vol.13, pp.291-295, 1997. ,
Assigning secondary structure from protein coordinate data, Proteins: Structure, Function, and Genetics, vol.234, issue.3, pp.313-320, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990515)35:3<313::AID-PROT5>3.0.CO;2-1
Helix geometry in proteins, Journal of Molecular Biology, vol.201, issue.3, pp.601-619, 1988. ,
DOI : 10.1016/0022-2836(88)90641-9
HELANAL: A Program to Characterize Helix Geometry in Proteins, Journal of Biomolecular Structure and Dynamics, vol.31, issue.5, pp.811-820, 2000. ,
DOI : 10.1107/S0021889891004399
Detection of secondary structure elements in proteins by hydrophobic cluster analysis, "Protein Engineering, Design and Selection", vol.5, issue.7, pp.629-635, 1992. ,
DOI : 10.1093/protein/5.7.629
Beyond the secondary structures : the structural alphabets Research signpost, pp.319-331, 2001. ,
Evaluating local structure alphabets for protein structure prediction, Ph.D. Computer Science, 2003. ,
A 3D building blocks approach to analyzing and predicting structure of proteins, Proteins: Structure, Function, and Genetics, vol.5, issue.4, pp.355-373, 1989. ,
DOI : 10.1002/prot.340050410
Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results, Proteins: Structure, Function, and Genetics, vol.14, issue.4, pp.430-439, 1992. ,
DOI : 10.1002/prot.340140404
The importance of short structural motifs in protein structure analysis, Journal of Computer-Aided Molecular Design, vol.6, issue.4, pp.457-472, 1993. ,
DOI : 10.1007/BF02337561
Local structural motifs of protein backbones are classified by self-organizing neural networks, "Protein Engineering, Design and Selection", vol.9, issue.10, pp.833-842, 1996. ,
DOI : 10.1093/protein/9.10.833
The complexity and accuracy of discrete state models of protein structure, Journal of Molecular Biology, vol.249, issue.2, pp.493-507, 1995. ,
DOI : 10.1006/jmbi.1995.0311
Small Libraries of Protein Fragments Model Native Protein Structures Accurately, Journal of Molecular Biology, vol.323, issue.2, pp.297-307, 2002. ,
DOI : 10.1016/S0022-2836(02)00942-7
Recurrent oligomers in proteins: An optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies, Proteins: Structure, Function, and Genetics, vol.105, issue.4, pp.662-674, 2000. ,
DOI : 10.1002/1097-0134(20000901)40:4<662::AID-PROT90>3.0.CO;2-F
Automatic definition of recurrent local structure motifs in proteins, Journal of Molecular Biology, vol.213, issue.2, pp.327-336, 1990. ,
DOI : 10.1016/S0022-2836(05)80194-9
Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme, Proteins: Structure, Function, and Genetics, vol.19, issue.2, pp.249-271, 1997. ,
DOI : 10.1002/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M
Prediction of local structure in proteins using a library of sequence-structure motifs, Journal of Molecular Biology, vol.281, issue.3, pp.565-577, 1998. ,
DOI : 10.1006/jmbi.1998.1943
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins: Structure, Function, and Genetics, vol.7, issue.3, pp.271-287, 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
Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.101, issue.1-3, pp.33-40, 1999. ,
DOI : 10.1007/s002140050402
Exploring the use of a structural alphabet for structural prediction of protein loops, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.106, issue.1-2, pp.28-35, 2001. ,
DOI : 10.1007/s002140100261
URL : https://hal.archives-ouvertes.fr/inserm-00134555
Compacting local protein folds with a "hybrid protein model", Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.106, issue.1-2, pp.36-47, 2001. ,
DOI : 10.1007/s002140000227
Hybrid Protein Model (HPM) : une nouvelle approche pour caractériser les relations séquence-structure dans les protéines, Premières Journées Ouvertes de Biologie, Informatique et Mathématiques. Recueil des Actes, pp.105-112, 2000. ,
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.2871-2886, 2002. ,
DOI : 10.1110/ps.0220502
URL : https://hal.archives-ouvertes.fr/inserm-00143374
Compactage d'une base de données protéiques recodées dans un alphabet structural, Secondes Journées Ouvertes de Biologie, Informatique et Mathématiques. Recueil des Actes, pp.85-92, 2001. ,
'Hybrid Protein Model' for optimally defining 3D protein structure fragments, Bioinformatics, vol.19, issue.3, pp.345-353, 2003. ,
DOI : 10.1093/bioinformatics/btf859
URL : https://hal.archives-ouvertes.fr/inserm-00133632
Hybrid Protein Model": a new clustering approach for 3D local structures, Proceedings of Workshop on Bioinformatics ISMIS. Chapter 5, pp.1-6, 2002. ,
URL : https://hal.archives-ouvertes.fr/inserm-00134559
Hybrid protein model (HPM): a method for building a library of overlapping local structural prototypes. Sensitivity study and improvements of the training, 2003 IEEE XIII Workshop on Neural Networks for Signal Processing (IEEE Cat. No.03TH8718), pp.53-70, 2003. ,
DOI : 10.1109/NNSP.2003.1318004
URL : https://hal.archives-ouvertes.fr/inserm-00133639
Rosetta in CASP4: Progress in ab initio protein structure prediction, Proteins: Structure, Function, and Genetics, vol.20, issue.S5, pp.119-126, 2001. ,
DOI : 10.1002/prot.1170
Ab Initio Protein Structure Prediction: Progress and Prospects, Annual Review of Biophysics and Biomolecular Structure, vol.30, issue.1, pp.173-189, 2001. ,
DOI : 10.1146/annurev.biophys.30.1.173
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.504-514, 2003. ,
DOI : 10.1002/prot.10369
Analysis, design and modification of loop regions in proteins, BioEssays, vol.188, issue.2-3, pp.63-69, 1988. ,
DOI : 10.1002/bies.950080205
Protein structural topology: automated analysis, diagrammatic representation and database HAL author manuscript inserm-00134564, 1999. ,
DOI : 10.1110/ps.8.4.897
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144300
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
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
A consensus view of fold space: combining SCOP, 2004. ,
The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues, Protein Engineering Design and Selection, vol.13, issue.3, pp.153-165, 2000. ,
DOI : 10.1093/protein/13.3.153
Assigning genomic sequences to CATH, Nucleic Acids Research, vol.28, issue.1, pp.277-282, 2000. ,
DOI : 10.1093/nar/28.1.277
URL : http://doi.org/10.1093/nar/28.1.277
Analysis of Domain Structural Class Using an Automated Class Assignment Protocol, Journal of Molecular Biology, vol.262, issue.2, pp.168-185, 1996. ,
DOI : 10.1006/jmbi.1996.0506
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), Nucleic Acids Research, vol.29, issue.1, pp.219-220, 2001. ,
DOI : 10.1093/nar/29.1.219
Selection of representative protein data sets, Protein Science, vol.11, issue.3, pp.409-417, 1992. ,
DOI : 10.1002/pro.5560010313
Enlarged representative set of protein structures, Protein Science, vol.2, issue.3, 1994. ,
DOI : 10.1002/pro.5560030317
PISCES: a protein sequence culling server, Bioinformatics, vol.19, issue.12, pp.1589-1591, 2003. ,
DOI : 10.1093/bioinformatics/btg224
The ASTRAL compendium for protein structure and sequence analysis, Nucleic Acids Research, vol.28, issue.1, pp.254-256, 2000. ,
DOI : 10.1093/nar/28.1.254
Self-organized formation of topologically correct feature maps, Biological Cybernetics, vol.13, issue.1, pp.59-69, 1982. ,
DOI : 10.1007/BF00337288
Self-Organizing Maps, 3rd edition, 2001. ,
A tutorial on Hidden Markov Models and selected applications in speech recognition, Proc. of the IEEE, pp.257-285, 1989. ,
Multivariate Analysis, 1979. ,
A non-linear mapping for data structure analysis, IEEE Transactions on Computers C, vol.18, pp.401-409, 1969. ,
A new method for analyzing protein sequence relationships based on Sammon maps, Protein Science, vol.18, issue.2, pp.287-293, 1997. ,
DOI : 10.1002/pro.5560060203
Classification of protein families and detection of the determinant residues with an improved self-organizing map, Biological Cybernetics, vol.76, issue.6, 1997. ,
DOI : 10.1007/s004220050357
HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins, Journal of Molecular Biology, vol.301, issue.1, pp.173-190, 2000. ,
DOI : 10.1006/jmbi.2000.3837
MOLMOL: A program for display and analysis of macromolecular structures, Journal of Molecular Graphics, vol.14, issue.1, pp.29-32, 1996. ,
DOI : 10.1016/0263-7855(96)00009-4