Helix capping, Protein Science, vol.31, issue.1, pp.21-38, 1998. ,
DOI : 10.1002/pro.5560070103
Protein Structure Prediction and Structural Genomics, Science, vol.294, issue.5540, pp.93-96, 2001. ,
DOI : 10.1126/science.1065659
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.82.1058
Helix geometry in proteins, Journal of Molecular Biology, vol.201, issue.3, pp.601-619, 1988. ,
DOI : 10.1016/0022-2836(88)90641-9
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
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
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
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
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
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
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
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
Hidden Markov model approach for identifying the modular framework of the protein backbone, Protein Engineering Design and Selection, vol.12, issue.12, pp.1063-1073, 1999. ,
DOI : 10.1093/protein/12.12.1063
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
Identification, classification, and analysis of beta-bulges in proteins, Protein Science, vol.170, issue.10, pp.1574-1590, 1993. ,
DOI : 10.1002/pro.5560021004
New methods for accurate prediction of protein secondary structure, Proteins: Structure, Function, and Genetics, vol.10, issue.3, pp.293-306, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990515)35:3<293::AID-PROT3>3.0.CO;2-L
Prediction and classification of ??-turn types, Biopolymers, vol.89, issue.7, pp.837-853, 1997. ,
DOI : 10.1002/(SICI)1097-0282(199712)42:7<837::AID-BIP9>3.0.CO;2-U
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.377-382, 1993. ,
DOI : 10.1093/protein/6.4.377
URL : https://hal.archives-ouvertes.fr/hal-00310605
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction, Proteins: Structure, Function, and Genetics, vol.266, issue.4, pp.508-519, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4
Hybrid Protein Model (HPM): a method to compact protein 3D-structure information and physicochemical properties, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000, pp.49-54, 2000. ,
DOI : 10.1109/SPIRE.2000.878179
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
Beyond the secondary structures: The structural alphabets, Recent Advances In Protein Engineering, pp.319-331, 2001. ,
Omega loops: Nonregular secondary structures significant in protein function and stability, FASEB J, vol.9, pp.708-717, 1995. ,
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
MODELLER: Generation and refinement of homology models, Methods Enzymol, 2001. ,
Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Genetics, vol.206, issue.4, pp.566-579, 1995. ,
DOI : 10.1002/prot.340230412
Enlarged representative set of protein structures, Protein Science, vol.2, issue.3, pp.522-524, 1994. ,
DOI : 10.1002/pro.5560030317
Selection of representative protein data sets, Protein Science, vol.11, issue.3, pp.409-417, 1992. ,
DOI : 10.1002/pro.5560010313
VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996. ,
DOI : 10.1016/0263-7855(96)00018-5
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
Fold prediction by a hierarchy of sequence, threading, and modeling methods, Protein Science, vol.12, issue.6, pp.1431-1440, 1998. ,
DOI : 10.1002/pro.5560070620
Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure, Proteins, vol.3, pp.104-111, 1999. ,
Enhanced genome annotation using structural profiles in the program 3D-PSSM, Journal of Molecular Biology, vol.299, issue.2, pp.499-520, 2000. ,
DOI : 10.1006/jmbi.2000.3741
Self-organized formation of topologically correct feature maps, Biological Cybernetics, vol.13, issue.1, pp.59-69, 1982. ,
DOI : 10.1007/BF00337288
MOLMOL: A program for display and analysis of macromolecular structures, Journal of Molecular Graphics, vol.14, issue.1, pp.51-55, 1996. ,
DOI : 10.1016/0263-7855(96)00009-4
Geometrical and Sequence Characteristics of ??-Helices in Globular Proteins, Biophysical Journal, vol.75, issue.4, pp.1935-1944, 1998. ,
DOI : 10.1016/S0006-3495(98)77634-9
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
P-SEA: a new efficient assignment of secondary structure from C?? trace of proteins, Bioinformatics, vol.13, issue.3, pp.291-295, 1997. ,
DOI : 10.1093/bioinformatics/13.3.291
Loops in globular proteins: a novel category of secondary structure, Science, vol.234, issue.4778, pp.849-855, 1986. ,
DOI : 10.1126/science.3775366
Linear programming optimization and a double statistical filter for protein threading protocols, Proteins: Structure, Function, and Genetics, vol.247, issue.3, pp.241-261, 2001. ,
DOI : 10.1002/prot.1145
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
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
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
Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction, Proteins: Structure, Function, and Genetics, vol.5, issue.S3, pp.149-170, 1999. ,
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<149::AID-PROT20>3.0.CO;2-H
Cascaded multiple classifiers for secondary structure prediction, Protein Science, vol.195, issue.2, pp.1162-1176, 2000. ,
DOI : 10.1110/ps.9.6.1162
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 protein secondary structure at 80% accuracy, Proteins: Structure, Function, and Genetics, vol.9, issue.1, pp.17-20, 2000. ,
DOI : 10.1002/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles, Proteins: Structure, Function, and Genetics, vol.47, issue.2, pp.228-235, 2002. ,
DOI : 10.1002/prot.10082
A tutorial on hidden Markov models and selected applications in speech recognition, Proceedings of the IEEE, vol.77, issue.2, pp.257-285, 1989. ,
DOI : 10.1109/5.18626
??-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
The beta bulge: a common small unit of nonrepetitive protein structure., Proc. Natl. Acad. Sci, pp.2574-2578, 1978. ,
DOI : 10.1073/pnas.75.6.2574
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
Models for the 3 10 -helix/coil, -helix-coil and -helix/3 10 -helix/coil transitions in isolated peptides, Protein Sci, vol.5, pp.1689-1696, 1996. ,
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
Turns in Peptides and Proteins, Adv. Protein Chem, vol.37, pp.1-109, 1985. ,
DOI : 10.1016/S0065-3233(08)60063-7
Review: Protein Secondary Structure Prediction Continues to Rise, Journal of Structural Biology, vol.134, issue.2-3, pp.204-218, 2001. ,
DOI : 10.1006/jsbi.2001.4336
Prediction of Protein Secondary Structure at Better than 70% Accuracy, Journal of Molecular Biology, vol.232, issue.2, pp.584-599, 1993. ,
DOI : 10.1006/jmbi.1993.1413
Protein secondary structure prediction using local alignments, Journal of Molecular Biology, vol.268, issue.1, pp.31-36, 1997. ,
DOI : 10.1006/jmbi.1997.0958
Comparative Protein Modelling by Satisfaction of Spatial Restraints, Journal of Molecular Biology, vol.234, issue.3, pp.779-815, 1993. ,
DOI : 10.1006/jmbi.1993.1626
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
[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
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions, Journal of Molecular Biology, vol.268, issue.1, pp.209-225, 1997. ,
DOI : 10.1006/jmbi.1997.0959
Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins: Structure, Function, and Genetics, vol.277, issue.S3, pp.171-176, 1999. ,
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
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
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
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
New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification, J. Mol. Biol, vol.289, pp.1469-1490, 1999. ,
Protein threading using PROSPECT: Design and evaluation, Proteins: Structure, Function, and Genetics, vol.14, issue.3, pp.343-354, 2000. ,
DOI : 10.1002/1097-0134(20000815)40:3<343::AID-PROT10>3.0.CO;2-S