The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain, Proceedings of the National Academy of Sciences, vol.37, issue.4, pp.205-211, 1951. ,
DOI : 10.1073/pnas.37.4.205
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
The discovery of the ??-helix and ??-sheet, the principal structural features of proteins, Proceedings of the National Academy of Sciences, vol.100, issue.20, pp.11207-11210, 2003. ,
DOI : 10.1073/pnas.2034522100
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
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
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
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods, BMC Structural Biology, vol.5, issue.1, p.17, 2005. ,
DOI : 10.1186/1472-6807-5-17
URL : https://hal.archives-ouvertes.fr/inserm-00090199
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins, Nucleic Acids Research, vol.32, issue.Web Server, pp.500-502, 2004. ,
DOI : 10.1093/nar/gkh429
Local Protein Structures, Current Bioinformatics, vol.2, issue.3, pp.165-202, 2007. ,
DOI : 10.2174/157489307781662105
URL : https://hal.archives-ouvertes.fr/inserm-00175058
2Struc: the secondary structure server, Bioinformatics, vol.26, issue.20, pp.2624-2625, 2010. ,
DOI : 10.1093/bioinformatics/btq480
: combining localization and description of protein secondary structure, Acta Crystallographica Section D Biological Crystallography, vol.12, issue.12, pp.1690-169310, 2012. ,
DOI : 10.1107/S0907444912039029
Analysis of loop boundaries using different local structure assignment methods, Protein Science, vol.34, issue.9, pp.1869-188110, 2009. ,
DOI : 10.1002/pro.198
URL : https://hal.archives-ouvertes.fr/inserm-00392504
Gibbs sampling and helix-cap motifs, Nucleic Acids Research, vol.33, issue.16, pp.5343-535333, 2005. ,
DOI : 10.1093/nar/gki842
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
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification, Journal of Molecular Biology, vol.289, issue.5, pp.1469-1490, 1999. ,
DOI : 10.1006/jmbi.1999.2826
Structural classification of ?????? and ?????? supersecondary structure units in proteins, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.193-212, 1998. ,
DOI : 10.1002/(SICI)1097-0134(19980201)30:2<193::AID-PROT9>3.0.CO;2-O
ArchDB 2014: structural classification of loops in proteins, Nucleic Acids Research, vol.42, issue.D1, pp.315-319, 2014. ,
DOI : 10.1093/nar/gkt1189
Assignment of PolyProline II Conformation and Analysis of Sequence ??? Structure Relationship, PLoS ONE, vol.59, issue.3, 2011. ,
DOI : 10.1371/journal.pone.0018401.s008
URL : https://hal.archives-ouvertes.fr/inserm-00586725
The Structure of Fibrous Proteins of the Collagen-Gelatin Group, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.272-281, 1951. ,
DOI : 10.1073/pnas.37.5.272
The Polypeptide Chain Configuration of Collagen, Nature, vol.176, issue.4492, pp.1062-1064, 1955. ,
DOI : 10.1021/ja01650a082
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
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
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
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
Polyproline-II Helix in Proteins: Structure and Function, Journal of Molecular Biology, vol.425, issue.12, pp.2100-2132, 2013. ,
DOI : 10.1016/j.jmb.2013.03.018
High accuracy prediction of ??-turns and their types using propensities and multiple alignments, Proteins: Structure, Function, and Bioinformatics, vol.55, issue.4, pp.828-839, 2005. ,
DOI : 10.1002/prot.20461
Protein beta-turn assignments, Bioinformation, vol.1, issue.5, pp.153-155, 2006. ,
DOI : 10.6026/97320630001153
URL : https://hal.archives-ouvertes.fr/inserm-00133658
The ?? Turn. Evidence for a New Folded Conformation in Proteins, Macromolecules, vol.5, issue.6, pp.818-819, 1972. ,
DOI : 10.1021/ma60030a031
Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites, J Mol Biol, vol.216, pp.386-397, 1990. ,
Alpha-turns in pro tein structures, Curr. Sci, vol.69, pp.434-447, 1995. ,
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
pi-Turns: types, systematics and the context of their occurrence in protein structures, BMC Structural Biology, vol.8, issue.1, pp.1472-6807, 2008. ,
DOI : 10.1186/1472-6807-8-39
??-Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence, Protein Science, vol.4, issue.5, pp.932-946, 1996. ,
DOI : 10.1002/pro.5560050515
The Anatomy and Taxonomy of Protein Structure, Adv Protein Chem, vol.34, pp.167-339, 1981. ,
DOI : 10.1016/S0065-3233(08)60520-3
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
The Reverse Turn as a Polypeptide Conformation in Globular Proteins, Proceedings of the National Academy of Sciences, vol.70, issue.2, pp.538-542, 1973. ,
DOI : 10.1073/pnas.70.2.538
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
A revised set of potentials for ??-turn formation in proteins, Protein Science, vol.3, issue.12, pp.2207-2216, 1994. ,
DOI : 10.1002/pro.5560031206
Analysis and prediction of the different types of ??-turn in proteins, Journal of Molecular Biology, vol.203, issue.1, pp.221-232, 1988. ,
DOI : 10.1016/0022-2836(88)90103-9
Identification, classification, and analysis of beta-bulges in proteins, Protein Science, vol.170, issue.10, pp.1574-1590, 1993. ,
DOI : 10.1002/pro.5560021004
? -turns in protein structures, Curr. Sci, vol.69, pp.434-447, 1995. ,
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
Standard conformations of a polypeptide chain in irregular protein regions], Mol Biol (Mosk), vol.20, pp.250-260, 1986. ,
Standard structures in proteins, Progress in Biophysics and Molecular Biology, vol.60, issue.3, pp.201-239, 1993. ,
DOI : 10.1016/0079-6107(93)90015-C
Super-secondary structures involving triple-strand ??-sheets, FEBS Letters, vol.211, issue.3, pp.253-256, 1993. ,
DOI : 10.1016/0014-5793(93)80688-Q
Super-secondary Structures and Modeling of Protein Folds, Methods Mol Biol, vol.932, pp.177-189, 2013. ,
DOI : 10.1007/978-1-62703-065-6_11
Structural trees for protein superfamilies, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.241-260, 1997. ,
DOI : 10.1002/(SICI)1097-0134(199706)28:2<241::AID-PROT12>3.0.CO;2-I
A structural tree for proteins containing 3??-corners, FEBS Letters, vol.247, issue.1, pp.37-41, 1997. ,
DOI : 10.1016/S0014-5793(97)00296-2
PCBOST: Protein classification based on structural trees, Biochemical and Biophysical Research Communications, vol.397, issue.3, pp.470-471, 2010. ,
DOI : 10.1016/j.bbrc.2010.05.136
-Turns and their distortions: a proposed new nomenclature, "Protein Engineering, Design and Selection", vol.3, issue.6, pp.479-493, 1990. ,
DOI : 10.1093/protein/3.6.479
URL : https://hal.archives-ouvertes.fr/hal-01209979
Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions, Proteins: Structure, Function, and Bioinformatics, vol.74, issue.Part 5, pp.353-36710, 2009. ,
DOI : 10.1002/prot.22185
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, 2001. ,
Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs, Journal of Chemical Information and Modeling, vol.49, issue.10, pp.2388-240210, 2009. ,
DOI : 10.1021/ci900202d
Prediction of turn types in protein structure by machine-learning classifiers, Proteins: Structure, Function, and Bioinformatics, vol.8, issue.2, pp.344-35210, 2009. ,
DOI : 10.1002/prot.22164
The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB, Proteins: Structure, Function, and Bioinformatics, vol.326, issue.Pt 5, pp.852-854, 2005. ,
DOI : 10.1002/prot.20394
Physical-chemical determinants of coil conformations in globular proteins, Protein Science, vol.326, issue.Suppl 8, pp.1127-1136399, 2010. ,
DOI : 10.1002/pro.399
Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints, Proceedings of the National Academy of Sciences, vol.108, issue.1, pp.109-1131014674107, 2011. ,
DOI : 10.1073/pnas.1014674107
PISCES: a protein sequence culling server, Bioinformatics, vol.19, issue.12, pp.1589-1591, 2003. ,
DOI : 10.1093/bioinformatics/btg224
Protein short loop prediction in terms of a structural alphabet, Computational Biology and Chemistry, vol.33, issue.4, pp.329-333, 2009. ,
DOI : 10.1016/j.compbiolchem.2009.06.002
URL : https://hal.archives-ouvertes.fr/inserm-00396485
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
A short survey on protein blocks, Biophysical Reviews, vol.30, issue.3, pp.137-145, 2010. ,
DOI : 10.1007/s12551-010-0036-1
URL : https://hal.archives-ouvertes.fr/inserm-00512823
A tutorial on hidden Markov models and selected application in speech recognition, Proceedings of the IEEE, pp.257-286, 1989. ,
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet, Nucleic Acids Research, vol.34, issue.Web Server, pp.119-123, 2006. ,
DOI : 10.1093/nar/gkl199
URL : https://hal.archives-ouvertes.fr/inserm-00133751
PBxplore: A program to explore protein structures with Protein Blocks Available at: https://github, PBxplore, pp.21-67, 2016. ,
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
'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
Sequence???structure relationship study in all-?? transmembrane proteins using an unsupervised learning approach, Amino Acids, vol.33, issue.7, pp.2303-2322, 2015. ,
DOI : 10.1007/s00726-015-2010-5
R: A Language for Data Analysis and Graphics, Journal of Computational and Graphical Statistics, vol.5, pp.299-314, 1996. ,
Stereochemistry of polypeptide chain configurations, Journal of Molecular Biology, vol.7, issue.1, pp.95-99, 1963. ,
DOI : 10.1016/S0022-2836(63)80023-6
Stereochemical Criteria for Polypeptide and Protein Chain Conformations, Biophysical Journal, vol.5, issue.6, pp.909-933, 1965. ,
DOI : 10.1016/S0006-3495(65)86759-5
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
Prediction of beta-turns, Biophysical Journal, vol.26, issue.3, pp.367-383, 1979. ,
DOI : 10.1016/S0006-3495(79)85259-5
platform for predicting and initiating ??-turns in a protein at desired locations, Proteins: Structure, Function, and Bioinformatics, vol.21, issue.5, pp.910-92110, 2015. ,
DOI : 10.1002/prot.24783
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
Beta-and gamma-turns in proteins revisited: a new set of amino acid turntype dependent positional preferences and potentials, J Biosci, vol.25, pp.143-156, 2000. ,
Standard structures in protein molecules. II. Beta-alpha hairpins], Mol Biol (Mosk), vol.20, pp.340-345, 1986. ,
Sparsely populated residue conformations in protein structures: Revisiting ???experimental??? Ramachandran maps, Proteins: Structure, Function, and Bioinformatics, vol.132, issue.7, pp.1101-111224384, 2014. ,
DOI : 10.1002/prot.24384
Kinetics and Thermodynamics of Type VIII ??-Turn Formation: A CD, NMR, and Microsecond Explicit Molecular Dynamics Study of the GDNP Tetrapeptide, Biophysical Journal, vol.90, issue.8, pp.2745-2759, 2006. ,
DOI : 10.1529/biophysj.105.074401
Conformational characteristics of asparaginyl residues in proteins, International Journal of Peptide and Protein Research, vol.7, issue.2, pp.112-122, 1994. ,
DOI : 10.1111/j.1399-3011.1994.tb00565.x
Analysis of gammabeta, betagamma, gammagamma, betabeta continuous turns in proteins, Journal of Peptide Research, vol.241, issue.4, pp.292-300, 2001. ,
DOI : 10.1093/bioinformatics/16.4.372
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
Bishistidyl Heme Hexacoordination, a Key Structural Property in Drosophila melanogaster Hemoglobin, Journal of Biological Chemistry, vol.280, issue.29, pp.27222-27229, 2005. ,
DOI : 10.1074/jbc.M503814200
X-ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and CoA: HOW THE ENZYME USES THE CYS-418 THIYL RADICAL FOR PYRUVATE CLEAVAGE, Journal of Biological Chemistry, vol.277, issue.42, pp.40036-40042, 2002. ,
DOI : 10.1074/jbc.M205821200
Carbon Monoxide Induced Decomposition of the Active Site [Ni???4Fe???5S] Cluster of CO Dehydrogenase, Journal of the American Chemical Society, vol.126, issue.17, pp.5382-538710, 2004. ,
DOI : 10.1021/ja037776v
Insights into Enzyme Evolution Revealed by the Structure of Methylaspartate Ammonia Lyase, Structure, vol.10, issue.1, pp.105-113, 2002. ,
DOI : 10.1016/S0969-2126(01)00696-7
Crystal Structure of Species D Adenovirus Fiber Knobs and Their Sialic Acid Binding Sites, Journal of Virology, vol.78, issue.14, pp.7727-77367727, 2004. ,
DOI : 10.1128/JVI.78.14.7727-7736.2004
On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding, Journal of Molecular Biology, vol.309, issue.1, pp.315-3304647, 2001. ,
DOI : 10.1006/jmbi.2001.4647
Crystal Structure of the (R)-Specific Enoyl-CoA Hydratase from Aeromonas caviae Involved in Polyhydroxyalkanoate Biosynthesis, Journal of Biological Chemistry, vol.278, issue.1, pp.617-62410, 2003. ,
DOI : 10.1074/jbc.M205484200
Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing, Structure, vol.13, issue.7, pp.973-984015, 2005. ,
DOI : 10.1016/j.str.2005.04.015
Structure and Mechanism of CTP:Phosphocholine Cytidylyltransferase (LicC) from Streptococcus pneumoniae, Journal of Biological Chemistry, vol.277, issue.6, pp.4343-4350, 2002. ,
DOI : 10.1074/jbc.M109163200
X-ray Structures of the Maltose???Maltodextrin-binding Protein of the Thermoacidophilic Bacterium Alicyclobacillus acidocaldarius Provide Insight into Acid Stability of Proteins, Journal of Molecular Biology, vol.335, issue.1, pp.261-274, 2004. ,
DOI : 10.1016/j.jmb.2003.10.042
Crystal Structure of the Amino-terminal Microtubule-binding Domain of End-binding Protein 1 (EB1), Journal of Biological Chemistry, vol.278, issue.38, pp.36430-3643410, 2003. ,
DOI : 10.1074/jbc.M305773200
The Structural Determination of Phosphosulfolactate Synthase from Methanococcus jannaschii at 1.7-A Resolution: AN ENOLASE THAT IS NOT AN ENOLASE, Journal of Biological Chemistry, vol.278, issue.46, pp.45858-4586310, 2003. ,
DOI : 10.1074/jbc.M307486200