The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information, Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, vol.35, issue.10, pp.2331-233910, 1107. ,
DOI : 10.1107/S0567740879009249
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
The protein data bank: A computer-based archival file for macromolecular structures, Journal of Molecular Biology, vol.112, issue.3, pp.535-542, 1977. ,
DOI : 10.1016/S0022-2836(77)80200-3
Hypothesis about the function of membrane-buried proline residues in transport proteins., Proceedings of the National Academy of Sciences, vol.83, issue.4, pp.917-921, 1986. ,
DOI : 10.1073/pnas.83.4.917
Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues, Biochemistry, vol.14, issue.22, pp.4953-4963, 1975. ,
DOI : 10.1021/bi00693a026
Autoinhibition of the Kit Receptor Tyrosine Kinase by the Cytosolic Juxtamembrane Region, Molecular and Cellular Biology, vol.23, issue.9, pp.3067-3078, 2003. ,
DOI : 10.1128/MCB.23.9.3067-3078.2003
On the Cis to Trans Isomerization of Prolyl???Peptide Bonds under Tension, The Journal of Physical Chemistry B, vol.116, issue.31, pp.9346-9351, 2012. ,
DOI : 10.1021/jp3042846
Conformational parameters for amino acids in helical, ??-sheet, and random coil regions calculated from proteins, Biochemistry, vol.13, issue.2, pp.211-222, 1974. ,
DOI : 10.1021/bi00699a001
Adaptive biasing force method for scalar and vector free energy calculations, The Journal of Chemical Physics, vol.128, issue.14, 2008. ,
DOI : 10.1063/1.2829861
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 native to amyloidogenic transition regulated by a backbone trigger, Nat Struct Mol Biol, vol.13, issue.3, pp.202-208, 1068. ,
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
PBOND: Web Server for the Prediction of Proline and Non-Proline cis/trans Isomerization, Genomics, Proteomics & Bioinformatics, vol.7, issue.3, pp.138-142, 2009. ,
DOI : 10.1016/S1672-0229(08)60042-X
Molecular dynamics simulation of ??2-microglobulin in denaturing and stabilizing conditions, Proteins: Structure, Function, and Bioinformatics, vol.1753, issue.3, pp.986-1001, 2011. ,
DOI : 10.1002/prot.22940
Structure of a cholesterol-binding protein deficient in Niemann-Pick type C2 disease, Proceedings of the National Academy of Sciences, vol.100, issue.5, pp.2512-2517, 2003. ,
DOI : 10.1073/pnas.0437840100
-conformation in protein structures on the basis of the amino acid sequence, FEBS Letters, vol.29, issue.1, pp.159-163, 1990. ,
DOI : 10.1016/0014-5793(90)80833-5
URL : https://hal.archives-ouvertes.fr/hal-01222357
The X-Pro peptide bond as an nmr probe for conformational studies of flexible linear peptides, Biopolymers, vol.14, issue.10, pp.2025-2041, 1976. ,
DOI : 10.1002/bip.1976.360151012
Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures, Journal of Molecular Biology, vol.264, issue.1, pp.191-198, 1996. ,
DOI : 10.1006/jmbi.1996.0633
Proline cis-trans isomerization in staphylococcal nuclease: Multi-substate free energy perturbation calculations, Protein Science, vol.22, issue.4, pp.636-654, 1995. ,
DOI : 10.1002/pro.5560040405
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143107
Two cis-prolines in the Bence-Jones protein Rei and the cis-pro-bend, FEBS Letters, vol.9, issue.2, pp.235-237, 1974. ,
DOI : 10.1016/0014-5793(74)80475-8
Kinetic folding and cis/trans prolyl isomerization of staphylococcal nuclease. A study by stoppedflow absorption, stopped-flow circular dichroism, and molecular dynamics simulations Non-proline cis peptide bonds in proteins, Biochemistry J Mol Biol, vol.36, issue.2861, pp.6529-6538291, 1997. ,
mRNA splicing, expression, and structure-function, Human Mutation, vol.32, issue.3, pp.237-246, 2010. ,
DOI : 10.1002/humu.21179
URL : https://hal.archives-ouvertes.fr/inserm-00448024
Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: effects on the structure of the beta3 subunit of the alphaIIbbeta3 integrin, PLoS ONE, vol.7, issue.11, 2012. ,
Protein secondary structure prediction based on position-specific scoring matrices, Journal of Molecular Biology, vol.292, issue.2, pp.195-202, 1999. ,
DOI : 10.1006/jmbi.1999.3091
A short survey on protein blocks, Biophysical Reviews, vol.30, issue.3, pp.137-147, 2010. ,
DOI : 10.1007/s12551-010-0036-1
URL : https://hal.archives-ouvertes.fr/inserm-00512823
Cis???trans peptide variations in structurally similar proteins, Amino Acids, vol.7, issue.5, pp.1369-1381, 2012. ,
DOI : 10.1007/s00726-011-1211-9
URL : https://hal.archives-ouvertes.fr/inserm-00680773
Conformational Preferences of Non-Prolyl and Prolyl Residues, The Journal of Physical Chemistry B, vol.110, issue.42, pp.21338-21348, 2006. ,
DOI : 10.1021/jp0647481
Replacement of a cis proline simplifies the mechanism of ribonuclease T1 folding, Biochemistry, vol.29, issue.27, pp.6475-6480, 1990. ,
DOI : 10.1021/bi00479a020
Effect of proline residues on protein folding, Journal of Molecular Biology, vol.145, issue.1, pp.251-263, 1981. ,
DOI : 10.1016/0022-2836(81)90342-9
Conservation of cis prolyl bonds in proteins during evolution, Proteins: Structure, Function, and Bioinformatics, vol.3, issue.3, pp.589-595, 2005. ,
DOI : 10.1002/prot.20342
Prolyl cis-trans isomerization as a molecular timer, Nature Chemical Biology, vol.32, issue.10, pp.619-629, 2007. ,
DOI : 10.1038/nchembio.2007.35
Cis???trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel, Nature, vol.84, issue.7065, pp.248-25210, 1038. ,
DOI : 10.1523/JNEUROSCI.2429-04.2004
Deviations from Planarity of the Peptide Bond in Peptides and Proteins, Journal of Molecular Biology, vol.264, issue.5, pp.1180-1195, 1996. ,
DOI : 10.1006/jmbi.1996.0705
Comparison of the predicted and observed secondary structure of T4 phage lysozyme, Biochimica et Biophysica Acta (BBA) - Protein Structure, vol.405, issue.2, pp.442-451, 1975. ,
DOI : 10.1016/0005-2795(75)90109-9
Receptor, The Journal of Physical Chemistry B, vol.113, issue.35, pp.12148-12153, 2009. ,
DOI : 10.1021/jp9046962
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
Proline Isomerization of Histone H3 Regulates Lysine Methylation and Gene Expression, Cell, vol.126, issue.5, pp.905-916, 2006. ,
DOI : 10.1016/j.cell.2006.07.026
Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence, BMC Structural Biology, vol.5, issue.1, pp.8-10, 2005. ,
DOI : 10.1186/1472-6807-5-8
COPS--Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information, Bioinformatics, vol.21, issue.5, pp.685-686, 2005. ,
DOI : 10.1093/bioinformatics/bti089
Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations, Journal of Molecular Biology, vol.294, issue.1, pp.271-288, 1999. ,
DOI : 10.1006/jmbi.1999.3217
The prolyl isomerase Pin1 regulates amyloid precursor protein processing and amyloid-?? production, Nature, vol.26, issue.7083, pp.528-534, 1038. ,
DOI : 10.1038/nature04543
A peptide model for proline isomerism in the unfolded state of staphylococcal nuclease, Journal of Molecular Biology, vol.228, issue.2, pp.338-342, 1992. ,
DOI : 10.1016/0022-2836(92)90822-2
Conformation of Polypeptides and Proteins, Adv Protein Chem, vol.23, pp.283-438, 1968. ,
DOI : 10.1016/S0065-3233(08)60402-7
Derivation of rules for comparative protein modeling from a database of protein structure alignments, Protein Science, vol.5, issue.9, pp.1582-1596, 1994. ,
DOI : 10.1002/pro.5560030923
Hinges, swivels and switches: the role of prolines in signalling via transmembrane ??-helices, Trends in Pharmacological Sciences, vol.21, issue.11, pp.445-451, 2000. ,
DOI : 10.1016/S0165-6147(00)01553-4
Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein, Molecular Cell, vol.25, issue.3, pp.413-426, 2007. ,
DOI : 10.1016/j.molcel.2007.01.004
Structural basis for regulation of the Crk signaling protein by a proline switch, Nature Chemical Biology, vol.462, issue.1, 2010. ,
DOI : 10.1038/nchembio.494
Acid catalysis of the formation of the slow-folding species of RNase A: Evidence that the reaction is proline isomerization, Proceedings of the National Academy of Sciences, vol.75, issue.10, pp.4764-4768, 1978. ,
DOI : 10.1073/pnas.75.10.4764
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information, BMC Bioinformatics, vol.7, issue.1, pp.124-134, 2006. ,
DOI : 10.1186/1471-2105-7-124
Occurrence and role ofcis peptide bonds in protein structures, Journal of Molecular Biology, vol.214, issue.1, pp.253-26010, 1990. ,
DOI : 10.1016/0022-2836(90)90159-J
Pin1 Regulates Centrosome Duplication, and Its Overexpression Induces Centrosome Amplification, Chromosome Instability, and Oncogenesis, Molecular and Cellular Biology, vol.26, issue.4, pp.1463-1479, 2006. ,
DOI : 10.1128/MCB.26.4.1463-1479.2006
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367188
proline isomerization and protein stability in staphylococcal nuclease, Protein Science, vol.9, issue.9, pp.1907-1916, 1996. ,
DOI : 10.1002/pro.5560050917
Structural insights into the catalytic mechanism of a family 18 exo-chitinase, Proceedings of the National Academy of Sciences, vol.98, issue.16, pp.8979-8984, 2001. ,
DOI : 10.1073/pnas.151103798
An overview of statistical learning theory, IEEE Transactions on Neural Networks, vol.10, issue.5, pp.988-999, 1999. ,
DOI : 10.1109/72.788640
The mean reaction force: A method to study the influence of the environment on reaction mechanisms, The Journal of Chemical Physics, vol.135, issue.6, 2011. ,
DOI : 10.1063/1.3624388
How Does Pin1 Catalyze the Cis???Trans Prolyl Peptide Bond Isomerization? A QM/MM and Mean Reaction Force Study, The Journal of Physical Chemistry B, vol.116, issue.43, pp.12972-12979, 2012. ,
DOI : 10.1021/jp307946h
Support vector machines for prediction of peptidyl prolyl cis/trans isomerization, The Journal of Peptide Research, vol.405, issue.1, pp.23-28100, 2004. ,
DOI : 10.1046/j.1399-3011.2004.00100.x
Peptide bonds revisited, Nature Structural & Molecular Biology, vol.3, issue.8, pp.676-686, 1998. ,
DOI : 10.1038/1368
peptide bonds may be important for factor XIII function, FEBS Letters, vol.24, issue.3, pp.291-296, 1998. ,
DOI : 10.1016/S0014-5793(98)00098-2
Local control of peptide conformation: Stabilization ofcis proline peptide bonds by aromatic proline interactions, 5\381:AID-BIP6[3.0.CO, pp.381-394, 1998. ,
DOI : 10.1002/(SICI)1097-0282(19980415)45:5<381::AID-BIP6>3.0.CO;2-H
Phosphorylation-specific prolyl isomerization: is there an underlying theme?, Nature Cell Biology, vol.5, issue.5, pp.435-441, 2005. ,
DOI : 10.1016/S0092-8674(03)00034-5
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates, Bioinformatics, vol.27, issue.15, pp.2076-2082, 2011. ,
DOI : 10.1093/bioinformatics/btr350
Intra- and Intermolecular Interaction Inducing Pyramidalization on Both Sides of a Proline Dipeptide during Isomerization: An Ab Initio QM/MM Molecular Dynamics Simulation Study in Explicit Water, Journal of the American Chemical Society, vol.131, issue.12, pp.4535-454010, 1021. ,
DOI : 10.1021/ja807814x