REFERENCES
- Fox A L. Tasteblindness. Science 1931; 73: 14
- Nebert D W. Pharmacogenetics: 65 candles on the cake. Pharmacogenetics 1997; 7: 435–440
- Snyder L H. Studies in human inheritance. IX. The inheritance of taste deficiency in man Ohio. J Sci 1932; 32: 436–440
- Bartoshuk L M, Duffy V B, Miller I J. PTC/PROP tasting: Anatomy, psychophysics, and sex effects. Physiol Behav 1994; 56: 1165–1171
- Drewnowski A, Rock C L. The influence of genetic taste markers on food acceptance. Am J Clin Nutr 1995; 62: 506–511
- Allison A C, Blumberg B S. Ability to taste phenylthiocarbamide among Alaskan Eskimos and other populations. Hum Biol 1959; 31: 352–359
- Kamphuis M MJW, Westerterp-Plantenga M S. PROP sensitivity affects macronutrient selection. Physiol Behav 2003; 79: 167–172
- Tepper B J, Nurse R J. Fat perception is related to PROP taster status. Physiol Behav 1997; 61: 949–954
- Kim U, Jorgenson E, Coon H, Leppert M, Risch N, Drayna D. Positional cloning of the human quantitative trait locus underlying taste sensitivity to phenylthiocarbamide. Science 2003; 299: 1221–1225
- Bufe B, Breslin P AS, Kuhn C, Reed D R, Tharp C D, Slack J P, Kim U K, Drayna D, Meyerhof W. The molecular basis of individual differences in phenylthiocarbamide and propylthiouracil bitterness perception. Curr Biol 2005; 15: 322–327
- Adler E, Hoon M A, Mueller K L, Chandrashekar J, Ryba N J, Zuker C S. A novel family of mammalian taste receptors. Cell 2000; 100: 693–702
- Bufe B, Hofmann T, Krautwurst D, Raguse J D, Meyerhof W. The human TAS2R16 receptor mediates bitter taste in response to β-glucopyranosides. Nat Genet 2002; 32: 397–401
- Damak S, Margolskee R F. G-proteins mediating taste transduction. Handb Cell Signal 2004; 2: 657–661
- Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N, Bourne P E. The protein databank. Nucleic Acids Res 2000; 28: 235–242
- Palczewski K, Kumasaka T, Hori T, Behnke C A, Motoshima H, Fox B A, Le Trong I, Teller D C, Okada T, Stenkamp R E. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 2000; 289: 739–45
- Nikiforovich G V, Galaktionov S, Balodis J, Marshall G R. Novel approach to computer modeling of seven-helical trans-membrane proteins: Current progress in the test case of bacteriorhodopsin. Acta Biochim Pol 2001; 48: 53–64
- Vaidehi N, Floriano W B, Trabanino R, Hall S E, Freddolino P, Choi E J, Zamanakos G, Goddard W A, III. Prediction of structure and function of G protein-coupled receptors. Proc Natl Acad Sci USA 2002; 99: 12622–12627
- Becker O M, Shacham S, Marantz Y, Noiman S. Modeling the 3D structure of GPCRs: Advances and application to drug discovery. Curr Opin Drug Disc Dev 2003; 6: 353–361
- Bissantz C, Bernard P, Hibert M, Rognan D. Protein-based virtual screening of chemical databases. II Are homology models of G-protein coupled receptors suitable targets?. Proteins 2003; 50: 5–25
- Cavasotto C N, Orry A JW, Abagyan R A. Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins 2003; 51: 423–433
- Yashar M, Kalani S, Vaidehi N, Hall S E, Trabanino R J, Freddolino P L, Kalani M A, Floriano W B, Wai V., Tak Kam V, Goddard G A, III. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. Proc Natl Acad Sci USA 2003; 101: 3815–3820
- Freddolino P L, Yashar M, Kalani S, Vaidehi N, Floriano W B, Hall S E, Trabanino R J, Wai Tak Kam V, Goddard W A, III. Predicted 3D structure for the human β-2 adrenergic receptor and its binding site for agonists and antagonists. Proc Natl Acad Sci USA 2004; 101: 2736–2741
- Montero C, Campillo N E, Goya P, Páez J A. Homology models of the cannabinoid CB1 and CB2 receptors. A docking analysis study. Eur J Med Chem 2005; 40: 75–83
- Cornette J L, Cease K B, Margalit H, Spouge J L, Berzofsky J A, DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J Mol Biol 1987; 195: 659–685
- Kyte J, Doolittle R F. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982; 157: 105–132
- Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 1984; 179: 125–142
- Tusnady G E, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics 2001; 17: 849–850
- Hirokawa T, Boon-Chieng S, Mitaku S. SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics 1988; 14: 378–379
- Juretic D, Lucic B, Zucic D, Trinajstic N. Protein transmembrane structure: Recognition and prediction by using hydrophobicity scales through preference functions. Theoretical and Computational Chemistry, C Parkanyi. Elsevier Science, Amsterdam 1988; 405–445
- Milpetz F, Argos P, Persson B. TMAP: A new email and WWW service for membrane-protein structural predictions. Trends Biochem Sci 1995; 20: 204–205
- Krogh A, Larsson B, von Heijne G, Sonnhammer E L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305: 567–580
- Hofmann K, Stoffel W. TMbase—A database of membrane spanning proteins segments. Biol Chem 1993; 374: 166–169
- Claros M G, von Heijne G. TopPred II: An improved software for membrane protein structure predictions. Comput Appl Biosci 1994; 10: 685–686
- Pashou E E, Litou Z I, Liakopoulos T D, Hamodrakas S J. WaveTM: Wavelet-based transmembrane segment prediction. In Silico Biol 2004; 4: 127–131
- Kelley L A, MacCallum R M, Sternberg M J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000; 299: 499–520
- Shi J, Blundell T L, Mizuguchi K. FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001; 310: 243–257
- Sippl M J. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995; 5: 229–235
- Levitt M. Competitive assessment of protein fold recognition and alignment accuracy. Proteins (Suppl) 1997; 1: 92–104
- Murzin A G. Structure classification-based assessment of CASP3 predictions for the fold recognition targets. Proteins 1999; 37: 88–103
- Bujnicki J M, Elofsson A, Fischer D, Rychlewski L. LiveBench-1: Continuous benchmarking of protein structure prediction servers. Protein Sci 2001; 10: 352–361
- Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2001; 119–130
- McGuffin L J, Jones D T. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 2001; 19: 874–881
- Vriend G. WHAT IF: A molecular modeling and drug design package. J Mol Graph 1990; 8: 52–56
- Tripos Inc., St. Louis, MO, Sybyl 6.9.
- Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 2: 4673–4680
- Mehler E L, Periole X, Hassan S A, Weinstein H. Key issues in the computational simulation of GPCR function: representation of loop domains. J Comput Aided Mol Des 2002; 16: 841–853
- Forrest L R, Woolf T B. Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions. Proteins 2003; 52: 492–509
- Feig M, Karanicolas J, Brooks C L, III. MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Mod 2004; 22: 377–395
- Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: Greater scalability for parallel molecular dynamics. J Comp Physiol [A] 1999; 151: 283–312
- Farrens D L, Altenbach C, Yang K, Hubbell W L, Khorana H G. Requirements of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 1996; 274: 768–770
- Campagne F, Jestin R, Reversat J L, Maigret B. Visualisation and integration of G protein-coupled receptor related information help the modeling: Description and applications of the Viseur program. J Comput Aided Mol Des 1999; 13: 625–643
- Shindyalov I N, Bourne P E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998; 11: 739–747
- Tripos Inc., St. Louis, MO, FlexX 2.2.18.
- CCDC Software Limited, Cambridge, UK, Gold 2.1.
- Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000; 295: 337–356
- Clark R D, Strizhev A, Leonard J M, Blakem J F, Matthew J B. Consensus scoring for ligand/protein interactions. J Mol Graph Mod 2002; 20: 281–295
- Eldridge M D, Murray C W, Auton T R, Paolini G V, Mee R P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 1997; 11: 425–445
- Meng E C, Shoichet B K, Kuntz I D. Automated docking with grid-based energy evaluation. J Comp Chem 2002; 13: 505–524
- Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996; 261: 470–489
- Jones G, Willett P, Glen R C, Leach A R, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997; 267: 727–748
- Muegge I, Martin Y C. A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J Med Chem 1999; 42: 791–804
- Mosberg H I, Fowler C B. Development and validation of opioid ligand-receptor interaction models: The structural basis of μ vs. δ selectivity. J Pept Res 2002; 60: 329–332
- Nelson T M, Munger S D, Boughter J D. Taste sensitivities to PROP and PTC vary independently in mice. Chem Sens 2003; 28: 695–704
- Avissar S, Amitai G, Sokolovsky M. Oligomeric structure of muscarinic receptors is shown by photoaffinity labeling. Proc Natl Acad Sci USA 1983; 80: 156–159
- Dean M, Higgs C, Smith R E, Bywater R P, Snell C R, Scott P D, Upton G JG, Howe T J, Reynolds C A. Dimerization of G-protein coupled receptors. J Med Chem 2001; 44: 4595–4614
- Arimoto R, Kisselev O G, Makara G M, Marshall G R. Rhodopsin-transducin interface: studies with conformationally constrained peptides. Biophys J 2001; 81: 3285–3293
- Meyer E A, Castellano R K, Diederich F. Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed 2003; 42: 1210–1250