Receptor databases and computational websites for ligand binding

Methods in Molecular Biology

Volumn 897, Issue , 2012, Pages 1-13

  Rana, Brinda K ^a   Bourne, Philip E ^b   Insel, Paul A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Binding prediction; Databases; GPCRs; Nuclear receptors

Indexed keywords

AMINO ACID; ANDROGEN RECEPTOR; BONE MORPHOGENETIC PROTEIN RECEPTOR; CELL NUCLEUS RECEPTOR; ESTROGEN RECEPTOR; G PROTEIN COUPLED RECEPTOR; GLUCOCORTICOID RECEPTOR; LIGAND GATED ION CHANNEL; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; RECEPTOR; RECEPTOR PROTEIN; STEROID RECEPTOR; THYROID HORMONE RECEPTOR; CELL RECEPTOR; LIGAND; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; CONFORMATION; DATA BASE; DATA MINING; DRUG BINDING; EXPRESSION VECTOR; GENETIC VARIABILITY; HUMAN; LIGAND BINDING; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PATTERN RECOGNITION; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEPTOR BINDING; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION; ANIMAL; BIOLOGY; COMPUTER PROGRAM; INTERNET; METABOLISM; METHODOLOGY; MOUSE; PROTEIN BINDING; PROTEIN DATABASE; RAT;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; INTERNET; LIGANDS; MICE; PROTEIN BINDING; PROTEINS; RATS; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RECEPTORS, G-PROTEIN-COUPLED; SOFTWARE;

EID: 84867306327     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-909-9_1     Document Type: Article

References (32)

1. Rana BK, Insel PA (2002) G-protein-coupled receptor websites. Trends Pharmacol Sci 23:535-536
2. Benson G (2010) Editorial. Nucleic Acids Research annual Web Server Issue in 2010. Nucleic Acids Res 38(Web Server Issue): W1-W2
3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242
4. Brooijmans N, Kuntz ID (2003) Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 32:335-373
5. Ewing TJA, Kuntz ID (1997) Critical evaluation of search algorithms used in automated molecular docking. J Comput Chem 18:1175-1189
6. Antes I (2010) DynaDock: a new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility. Proteins 78:1084-1104
7. Hendlich M, Bergner A, Gunther J, Klebe G (2003) Relibase: design and development of a database for comprehensive analysis of pro-tein-ligand interactions. J Mol Biol 326: 607-620
8. Roche O, Kiyama R, Books CL (2001) Ligand-Protein DataBase: linking protein-ligand complex structures to binding data. J Med Chem 44:3592-3598
9. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15: 411-428
10. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 19:1639-1662
11. Zsoldos Z, Reid D, Simon A, Sadjad BS, Johnson AP (2006) eHiTS: an innovative approach to the docking and scoring function problems. Curr Protein Pept Sci 7:421-435
12. Chen X, Ji ZL, Zhi DG, Chen YZ (2002) CLiBE: a database of computed ligand binding energy for ligand-receptor complexes and its potential use in the analysis of drug binding competitiveness. J Comput Chem 26: 661-666
13. Chen YZ, Gu XL, Cao ZW (2001) Can an optimization/scoring procedure in ligand-protein docking be employed to probe drug-resistant mutations in proteins? J Mol Graph Model 19:560-570
14. Chen YZ, Ung CY (2001) Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach. J Mol Graph Model 20:199-218
15. Stuart AC, Ilyin VA, Sali A (2002) LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18:200-201
16. Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8:127-134
17. Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method de fines binding surfaces common to protein families. J Mol Biol 257:342-358
18. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 31:294-197
19. Beukers MW, Kristiansen K, Ijzerman AP, Edvardsen O (1999) TinyGRAP database: a bioinformatics tool to mine G protein-coupled receptor mutant data. Trends Pharmacol Sci 20:475-477
20. Takeda S, Kadowaki S, Haga T, Takaesu H, Mitaku S (2002) Identi fication of G protein-coupled receptor genes from the human genome sequence. FEBS Lett 520:97-101
21. Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63:1256-1272
22. Crasto C, Marenco L, Miller PL, Shepherd GS (2002) Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Res 30:354-360
23. Martinez E, Moore DD, Keller E, Pearce D, Vanden Heuvel JP, Robinson V, Bottlieb B, MacDonald P, Simons S Jr, Sanchez E, Danielsen M (1998) The nuclear receptor resource: a growing family. Nucleic Acids Res 26:239-241
24. Horn F, Vriend G, Cohen FE (2001) Collecting and harvesting biological data: the GPCRDB & NucleaRDB databases. Nucleic Acids Res 29:346-349
25. Bettler E, Krause R, Horn F, Vriend G (2003) NRSAS: Nuclear Receptor Structure Analysis Servers. Nucleic Acids Res 31:3400-3403
26. Van Durme JJ, Bettler E, Folkertsma S, Horn F, Vriend G (2003) NRMD: Nuclear Receptor Mutation Database. Nucleic Acids Res 31: 331-333
27. Ben-Shlomo I, Yu Hsu S, Rauch R, Kowalski HW, Hsueh AJ (2003) Signaling receptome: a genomic and evolutionary perspective of plasma membrane receptors involved in signal trans-duction. Sci STKE 17(187):RE9
28. Le Novere N, Changeux J-P (1999) The ligand gated ion channel database. Nucleic Acids Res 27:340-342
29. Graeber TG, Eisenberg D (2001) Bioinformatic identi fication of potential autocrine signaling loops in cancer using gene expression pro files. Nat Genet 29:295-300
30. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim S, Eisenberg D (2002) DIP: the Database of Interacting Proteins. A research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30:303-305
31. Bauer RA, Günther S, Jansen D, Heeger C, Thaben PF, Preissner R (2009) SuperSite: dictionary of metabolite and drug binding sites in proteins. Nucleic Acids Res 37:D195-D200
32. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31: 19-20