Estimation of membrane proteins in the human proteome, In Silico Biol, vol.6, pp.379-386, 2006. ,
fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix, Journal of Molecular Biology, vol.270, issue.3, pp.481-495, 1997. ,
DOI : 10.1006/jmbi.1997.1114
Study and Prediction of Secondary Structure for Membrane Proteins, Journal of Biomolecular Structure and Dynamics, vol.12, issue.4, pp.421-428, 2007. ,
DOI : 10.1080/07391102.2007.10507130
Comprehensive analysis of transmembrane topologies in prokaryotic genomes, Gene, vol.304, pp.77-86, 2003. ,
DOI : 10.1016/S0378-1119(02)01181-2
Computational analysis of membrane proteins: the largest class of drug targets, Drug Discovery Today, vol.14, issue.23-24, pp.1130-1135, 2009. ,
DOI : 10.1016/j.drudis.2009.08.006
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins, BMC Bioinformatics, vol.7, issue.1, p.189, 2006. ,
DOI : 10.1186/1471-2105-7-189
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
G protein-coupled receptors: In silico drug discovery in 3D, Proceedings of the National Academy of Sciences, vol.101, issue.31, pp.11304-11309, 2004. ,
DOI : 10.1073/pnas.0401862101
Description of the local protein structure. I. Classical approaches, Recent Adv, pp.1-33, 2007. ,
URL : https://hal.archives-ouvertes.fr/inserm-00176471
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins, Bioinformatics, vol.20, issue.12, pp.1822-1835, 2004. ,
DOI : 10.1093/bioinformatics/bth143
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles, Bioinformatics, vol.22, issue.3, pp.303-309, 2006. ,
DOI : 10.1093/bioinformatics/bti784
Transmembrane helix predictions revisited, Protein Science, vol.34, issue.Suppl 5, pp.2774-2791, 2002. ,
DOI : 10.1110/ps.0214502
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373751
Long membrane helices and short loops predicted less accurately, Protein Science, vol.20, issue.12, pp.2766-2773, 2002. ,
DOI : 10.1110/ps.0214602
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373740
State-of-the-art in membrane protein prediction, Appl Bioinformatics, vol.1, pp.21-35, 2002. ,
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
Properties of polyproline II, a secondary structure element implicated in protein-protein interactions, Proteins: Structure, Function, and Bioinformatics, vol.179, issue.4, pp.880-892, 2005. ,
DOI : 10.1002/prot.20327
Secondary structure assignment that accurately reflects physical and evolutionary characteristics, BMC Bioinformatics, vol.6, issue.Suppl 4, 2005. ,
DOI : 10.1186/1471-2105-6-S4-S8
URL : http://doi.org/10.1186/1471-2105-6-s4-s8
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
Transmembrane helix prediction: a comparative evaluation and analysis, Protein Engineering Design and Selection, vol.18, issue.6, pp.295-308, 2005. ,
DOI : 10.1093/protein/gzi032
New assessment of Protein Blocks, In Silico Biology, vol.5, pp.283-289, 2005. ,
Editorial [Hot Topic: In Silico (Guest Editor: Alexandre G. de Brevern)], Infectious Disorders - Drug Targets, vol.9, issue.3, pp.246-247, 2009. ,
DOI : 10.2174/1871526510909030246
In Silico Studies on DARC, silico studies on DARC, pp.289-303, 2009. ,
DOI : 10.2174/1871526510909030289
URL : https://hal.archives-ouvertes.fr/inserm-00366309
???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
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
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
A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC), Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1724, issue.3, pp.288-306, 2005. ,
DOI : 10.1016/j.bbagen.2005.05.016
URL : https://hal.archives-ouvertes.fr/inserm-00143373
Customizing G Protein-Coupled Receptor Models for Structure-Based Virtual Screening, Current Pharmaceutical Design, vol.15, issue.35, pp.4026-4048, 2009. ,
DOI : 10.2174/138161209789824786
Different Membrane Anchoring Positions of Tryptophan and Lysine in Synthetic Transmembrane ??-Helical Peptides, Journal of Biological Chemistry, vol.274, issue.30, pp.20839-20846, 1999. ,
DOI : 10.1074/jbc.274.30.20839
The PyMOL Molecular Graphics System DeLano Scientific, 2002. ,
Protein secondary structure assignment through Vorono?? tessellation, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.3, pp.519-528, 2004. ,
DOI : 10.1002/prot.10566
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.138.3512
Membrane Protein Structure: Prediction versus Reality, Annual Review of Biochemistry, vol.76, issue.1, pp.125-140, 2007. ,
DOI : 10.1146/annurev.biochem.76.052705.163539
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.332.4023
Assigning transmembrane segments to helices in intermediate-resolution structures, Bioinformatics, vol.20, issue.Suppl 1, pp.122-129, 2004. ,
DOI : 10.1093/bioinformatics/bth939
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/suppl_1/i122
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
Side-chain Contributions to Membrane Protein Structure and Stability, Journal of Molecular Biology, vol.335, issue.1, pp.297-305, 2004. ,
DOI : 10.1016/j.jmb.2003.10.041
Progress in structure prediction of ??-helical membrane proteins, Current Opinion in Structural Biology, vol.16, issue.4, pp.496-504, 2006. ,
DOI : 10.1016/j.sbi.2006.06.003
Transmembrane protein structures without X-rays, Trends in Biochemical Sciences, vol.31, issue.2, pp.106-113, 2006. ,
DOI : 10.1016/j.tibs.2005.12.005
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
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
Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Genetics, vol.206, issue.4, pp.566-579, 1995. ,
DOI : 10.1002/prot.340230412
Electron-crystallographic Refinement of the Structure of Bacteriorhodopsin, Journal of Molecular Biology, vol.259, issue.3, pp.393-421, 1996. ,
DOI : 10.1006/jmbi.1996.0328
Discrimination of outer membrane proteins using machine learning algorithms, Proteins: Structure, Function, and Bioinformatics, vol.46, issue.4, pp.1031-1037, 2006. ,
DOI : 10.1002/prot.20929
Structural Determinants of Transmembrane Helical Proteins, Structure, vol.17, issue.8, pp.1092-1103, 2009. ,
DOI : 10.1016/j.str.2009.06.009
PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C?? atoms, Computational Biology and Chemistry, vol.32, issue.6, pp.406-411, 2008. ,
DOI : 10.1016/j.compbiolchem.2008.07.027
R: a language for data analysis and graphics, J Comput Graph Stat, vol.5, pp.299-314, 1996. ,
Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies, In Silico Biol, vol.2, pp.19-33, 2002. ,
TMPDB: a database of experimentally-characterized transmembrane topologies, Nucleic Acids Research, vol.31, issue.1, pp.406-409, 2003. ,
DOI : 10.1093/nar/gkg020
The 7???TM G-Protein-Coupled Receptor Target Family, ChemMedChem, vol.427, issue.8, pp.761-782, 2006. ,
DOI : 10.1002/cmdc.200600134
Do transmembrane protein superfolds exist?, FEBS Letters, vol.272, issue.3, pp.281-285, 1998. ,
DOI : 10.1016/S0014-5793(98)00095-7
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
Improving the accuracy of transmembrane protein topology prediction using evolutionary information, Bioinformatics, vol.23, issue.5, pp.538-544, 2007. ,
DOI : 10.1093/bioinformatics/btl677
Local Structure Alphabets, Protein Structure Prediction (eds. H. Rangwala, and G. Karypis), pp. in press, 2010. ,
URL : https://hal.archives-ouvertes.fr/inserm-00557300
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
A Combined Transmembrane Topology and Signal Peptide Prediction Method, Journal of Molecular Biology, vol.338, issue.5, pp.1027-1036, 2004. ,
DOI : 10.1016/j.jmb.2004.03.016
An HMM posterior decoder for sequence feature prediction that includes homology information, Bioinformatics, vol.21, issue.Suppl 1, pp.251-257, 2005. ,
DOI : 10.1093/bioinformatics/bti1014
Coils in the Membrane Core Are Conserved and Functionally Important, Journal of Molecular Biology, vol.380, issue.1, pp.170-180, 2008. ,
DOI : 10.1016/j.jmb.2008.04.052
Static benchmarking of membrane helix predictions, Nucleic Acids Research, vol.31, issue.13, pp.3642-3644, 2003. ,
DOI : 10.1093/nar/gkg532
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
MetaTM - a consensus method for transmembrane protein topology prediction, BMC Bioinformatics, vol.10, issue.1, p.314, 2009. ,
DOI : 10.1186/1471-2105-10-314
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, p.501, 2001. ,
Unlocking the molecular secrets of sodium-coupled transporters, Nature, vol.30, issue.7245, pp.347-355, 2009. ,
DOI : 10.1038/nature08143
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-580, 2001. ,
DOI : 10.1006/jmbi.2000.4315
On Information and Sufficiency, The Annals of Mathematical Statistics, vol.22, issue.1, pp.79-86, 1951. ,
DOI : 10.1214/aoms/1177729694
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
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
Determining membrane protein structures: still a challenge!, Trends in Biochemical Sciences, vol.32, issue.6, pp.259-270, 2007. ,
DOI : 10.1016/j.tibs.2007.04.001
URL : https://hal.archives-ouvertes.fr/hal-00258998
Drugs and their molecular targets: an updated overview, Fundamental & Clinical Pharmacology, vol.1171, issue.1, pp.1-18, 2008. ,
DOI : 10.1016/j.tips.2006.12.006
URL : https://hal.archives-ouvertes.fr/hal-00246545
Membrane protein structure quality in molecular dynamics simulation, Journal of Molecular Graphics and Modelling, vol.24, issue.2, pp.157-165, 2005. ,
DOI : 10.1016/j.jmgm.2005.05.006
UniProt archive, Bioinformatics, vol.20, issue.17, pp.3236-3237, 2004. ,
DOI : 10.1093/bioinformatics/bth191
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/17/3236
Positioning of proteins in membranes: A computational approach, Protein Science, vol.77, issue.6, pp.1318-1333, 2006. ,
DOI : 10.1110/ps.062126106
OPM: Orientations of Proteins in Membranes database, Bioinformatics, vol.22, issue.5, pp.623-625, 2006. ,
DOI : 10.1093/bioinformatics/btk023
The three-dimensional structure of HLA-B27 at 2.1 ?? resolution suggests a general mechanism for tight peptide binding to MHC, Cell, vol.70, issue.6, pp.1035-1048, 1992. ,
DOI : 10.1016/0092-8674(92)90252-8
PALSSE: A program to delineate linear secondary structural elements from protein structures, BMC Bioinformatics, vol.6, issue.1, p.202, 2005. ,
DOI : 10.1186/1471-2105-6-202
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins, Bioinformatics, vol.19, issue.Suppl 1, pp.205-211, 2003. ,
DOI : 10.1093/bioinformatics/btg1027
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
Evaluation of methods for the prediction of membrane spanning regions, Bioinformatics, vol.17, issue.7, pp.646-653, 2001. ,
DOI : 10.1093/bioinformatics/17.7.646
A collection of well characterised integral membrane proteins, Bioinformatics, vol.16, issue.12, pp.1159-1160, 2000. ,
DOI : 10.1093/bioinformatics/16.12.1159
Molecular models of the open and closed states of the whole human CFTR protein, Cellular and Molecular Life Sciences, vol.25, issue.21, pp.3469-3486, 2009. ,
DOI : 10.1007/s00018-009-0133-0
URL : https://hal.archives-ouvertes.fr/hal-00417499
A general protocol for the crystallization of membrane proteins for X-ray structural investigation, Nature Protocols, vol.189, issue.5, pp.619-637, 2009. ,
DOI : 10.1038/nprot.2009.27
Rationalizing ??-helical membrane protein crystallization, Protein Science, vol.59, issue.3, pp.466-472, 2008. ,
DOI : 10.1110/ps.073263108
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248303
Prediction of partial membrane protein topologies using a consensus approach, Protein Science, vol.32, issue.12, pp.2974-2980, 2002. ,
DOI : 10.1110/ps.0226702
Transmembrane protein topology prediction using support vector machines, BMC Bioinformatics, vol.10, issue.1, p.159, 2009. ,
DOI : 10.1186/1471-2105-10-159
URL : http://doi.org/10.1186/1471-2105-10-159
A limited universe of membrane protein families and folds, Protein Science, vol.7, issue.7, pp.1723-1734, 2006. ,
DOI : 10.1110/ps.062109706
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor, Science, vol.289, issue.5480, pp.739-745, 2000. ,
DOI : 10.1126/science.289.5480.739
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 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
A tutorial on hidden Markov models and selected applications in speech recognition, Proceedings of the IEEE, vol.77, issue.2, pp.257-286, 1989. ,
DOI : 10.1109/5.18626
svmPRAT: SVM-based Protein Residue Annotation Toolkit, BMC Bioinformatics, vol.10, issue.1, p.439, 2009. ,
DOI : 10.1186/1471-2105-10-439
URL : http://doi.org/10.1186/1471-2105-10-439
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
Non-??-helical elements modulate polytopic membrane protein architecture11Edited by G. Von Heijne, Journal of Molecular Biology, vol.306, issue.2, pp.349-362, 2001. ,
DOI : 10.1006/jmbi.2000.4402
Structural details (kinks and non-?? conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors, Nucleic Acids Research, vol.31, issue.15, pp.4625-4631, 2003. ,
DOI : 10.1093/nar/gkg639
New Roles for a Key Glycine and Its Neighboring Residue in Potassium Channel Gating, Biophysical Journal, vol.91, issue.8, pp.2860-2873, 2006. ,
DOI : 10.1529/biophysj.105.080242
Topology prediction for helical transmembrane proteins at 86% accuracy-Topology prediction at 86% accuracy, Protein Science, vol.227, issue.8, pp.1704-1718, 1996. ,
DOI : 10.1002/pro.5560050824
Redefining the goals of protein secondary structure prediction, Journal of Molecular Biology, vol.235, issue.1, pp.13-26, 1994. ,
DOI : 10.1016/S0022-2836(05)80007-5
Data-driven model for the prediction of protein transmembrane regions, SAR and QSAR in Environmental Research, vol.4, issue.7-8, pp.741-754, 2009. ,
DOI : 10.1186/1471-2105-7-189
A nonlinear mapping for data structure analysis, IEEE Transactions on Computers, vol.18, pp.401-409, 1969. ,
Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.14808-14813, 2008. ,
DOI : 10.1073/pnas.0803103105
PREDICT modeling and in-silico screening for G-protein coupled receptors, Proteins: Structure, Function, and Bioinformatics, vol.21, issue.2-3, pp.51-86, 2004. ,
DOI : 10.1002/prot.20195
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
Are membrane proteins ?inside-out? proteins?, Proteins: Structure, Function, and Genetics, vol.366, issue.1, pp.135-143, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990701)36:1<135::AID-PROT11>3.0.CO;2-I
New method for protein secondary structure assignment based on a simple topological descriptor, Proteins: Structure, Function, and Bioinformatics, vol.7, issue.1, pp.513-524, 2005. ,
DOI : 10.1002/prot.20471
A method for ??-helical integral membrane protein fold prediction, Proteins: Structure, Function, and Genetics, vol.225, issue.3, pp.281-294, 1994. ,
DOI : 10.1002/prot.340180309
Pex, analytical tools for PDB files. I. GF-Pex: Basic file to describe a protein, Proteins: Structure, Function, and Genetics, vol.302, issue.1, pp.28-36, 2001. ,
DOI : 10.1002/1097-0134(20010401)43:1<28::AID-PROT1014>3.0.CO;2-M
Transmembrane proteins in the Protein Data Bank: identification and classification, Bioinformatics, vol.20, issue.17, pp.2964-2972, 2004. ,
DOI : 10.1093/bioinformatics/bth340
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank, Nucleic Acids Research, vol.33, issue.Database issue, pp.275-278, 2005. ,
DOI : 10.1093/nar/gki002
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates, Bioinformatics, vol.21, issue.7, pp.1276-1277, 2005. ,
DOI : 10.1093/bioinformatics/bti121
Principles governing amino acid composition of integral membrane proteins: application to topology prediction, Journal of Molecular Biology, vol.283, issue.2, pp.489-506, 1998. ,
DOI : 10.1006/jmbi.1998.2107
The HMMTOP transmembrane topology prediction server, Bioinformatics, vol.17, issue.9, pp.849-850, 2001. ,
DOI : 10.1093/bioinformatics/17.9.849
Analysis of loop boundaries using different local structure assignment methods, Protein Science, vol.34, issue.9, pp.1869-1881, 2009. ,
DOI : 10.1002/pro.198
URL : https://hal.archives-ouvertes.fr/inserm-00392504
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
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.32-39, 2006. ,
DOI : 10.1002/prot.21087
URL : https://hal.archives-ouvertes.fr/inserm-00133760
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
Helical membrane proteins: diversity of functions in the context of simple architecture, Current Opinion in Structural Biology, vol.11, issue.3, pp.370-376, 2001. ,
DOI : 10.1016/S0959-440X(00)00217-7
The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Research, vol.38, issue.Database, pp.142-148, 2010. ,
DOI : 10.1093/nar/gkp846
Prediction of structure and function of G proteincoupled receptors, Proc Natl Acad Sci, vol.3, issue.99, pp.12622-12627, 2002. ,
Best ??-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information, Protein Science, vol.12, issue.7, pp.1908-1917, 2004. ,
DOI : 10.1110/ps.04625404
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279939
Membrane-protein topology, Nature Reviews Molecular Cell Biology, vol.13, issue.12, pp.909-918, 2006. ,
DOI : 10.1038/nrm2063
Topogenic signals in integral membrane proteins, European Journal of Biochemistry, vol.1, issue.4, pp.671-678, 1988. ,
DOI : 10.1146/annurev.biochem.55.1.511
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms, Protein Science, vol.271, issue.4, pp.1029-1038, 1998. ,
DOI : 10.1002/pro.5560070420
The progress of membrane protein structure determination, Protein Science, vol.185, issue.7, pp.1948-1949, 2004. ,
DOI : 10.1110/ps.04712004
Biophysical dissection of membrane proteins, Nature, vol.15, issue.7245, pp.344-346, 2009. ,
DOI : 10.1038/nature08142
How Membranes Shape Protein Structure, Journal of Biological Chemistry, vol.276, issue.35, pp.32395-32398, 2001. ,
DOI : 10.1074/jbc.R100008200
Transmembrane helices before, during, and after insertion, Current Opinion in Structural Biology, vol.15, issue.4, pp.378-386, 2005. ,
DOI : 10.1016/j.sbi.2005.07.004
MEMBRANE PROTEIN FOLDING AND STABILITY: Physical Principles, Annual Review of Biophysics and Biomolecular Structure, vol.28, issue.1, pp.319-365, 1999. ,
DOI : 10.1146/annurev.biophys.28.1.319
Multipass membrane protein structure prediction using Rosetta, Proteins: Structure, Function, and Bioinformatics, vol.289, issue.5480, pp.1010-1025, 2006. ,
DOI : 10.1002/prot.20817
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479309
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors, Proceedings of the National Academy of Sciences, vol.101, issue.4, pp.959-963, 2004. ,
DOI : 10.1073/pnas.0306077101
Proline Substitutions are not Easily Accommodated in a Membrane Protein, Journal of Molecular Biology, vol.341, issue.1, pp.1-6, 2004. ,
DOI : 10.1016/j.jmb.2004.06.025
A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment, Proteins: Structure, Function, and Genetics, vol.1, issue.2, pp.220-223, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K
Structure Modeling of All Identified G Protein???Coupled Receptors in the Human Genome, PLoS Computational Biology, vol.20, issue.2, p.13, 2006. ,
DOI : 0376-5067(1995)020[0374:RBGFA]2.0.CO;2
An amino acid ???transmembrane tendency??? scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity, Protein Science, vol.225, issue.8, pp.1987-2001, 2006. ,
DOI : 10.1110/ps.062286306
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method, Protein Science, vol.49, issue.7, pp.1547-1555, 2003. ,
DOI : 10.1110/ps.0305103
Precise annotation of transmembrane segments with Garlic -a free molecular visualization program, Croatica Chemica Acta, vol.77, pp.397-401, 2004. ,