Internet resources in GPCR modellingFootnote1

¹Presented at CMTPI 2007: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Moscow, Russia, September 1–5, 2007).

References

• Flower , DR . 1999 . Modelling G-protein-coupled receptors for drug design . Biochim. Biophys. Acta. , 1422 : 207 – 234 .
   PubMed Web of Science ®Google Scholar
• Klabunde , T and Hessler , G . 2002 . Drug design strategies for targeting G-protein-coupled receptors . Chem. Bio. Chem. , 3 : 928 – 944 .
   Google Scholar
• Zhang , Y , DeVries , ME and Skolnick , J . 2006 . Structure modeling of all identified G protein-coupled receptors in the human genome . PLoS. Comput. Biol. , 2 : e13
   PubMed Web of Science ®Google Scholar
• Sali , A and Blundell , TL . 1993 . Comparative protein modeling by satisfaction of spatial restraints . J. Mol. Biol. , 234 : 779 – 815 .
   PubMed Web of Science ®Google Scholar
• Marti-Renom , MA , Stuart , AC and Fiser , A . 2000 . Comparative protein structure modeling of genes and genomes . Ann. Rev. Biophys. Biomol. Struct. , 29 : 291 – 325 .
   PubMedGoogle Scholar
• Liwo , A . 1999 . Protein structure prediction by global optimization of a potential energy function . Proc. Natl. Acad. Sci. U.S.A. , 96 : 5482 – 5485 .
   Google Scholar
• Gasteiger , E . 2003 . ExPASy: the proleomics server for in-depth protein knowledge and analysis . Nucl. Acid. Res. , 31 : 3784 – 3788 .
   PubMed Web of Science ®Google Scholar
• Lipman , DJ and Pearson , WR . 1985 . Rapid and sensitive protein similarity searches . Science , 227 : 1435 – 1441 .
   PubMed Web of Science ®Google Scholar
• Altschul , SF . 1997 . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs . Nucleic Acids Res. , 25 : 3389 – 3402 .
   PubMed Web of Science ®Google Scholar
• Thompson , JD , Higgins , DG and Gibson , TJ . 1994 . CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice . Nucleic Acids Res. , 22 : 4673 – 4680 .
   PubMed Web of Science ®Google Scholar
• Notredame , C , Higgins , DG and Heringa , J . 2000 . T-Coffee: a novel method for fast and accurate multiple sequence alignment . J. Mol. Biol. , 302 : 205 – 217 .
   PubMed Web of Science ®Google Scholar
• Hill , SJ . 1997 . International Union of Pharmacology. XIII. Classification of histamine receptors . Pharmacol. Rev. , 49 : 253 – 278 .
   PubMed Web of Science ®Google Scholar
• Kiss , R , Zoltan , K and Keseru , GM . 2004 . Homology modelling and binding site mapping of the human histamine HI receptor . Eur. J. Med. Chem. , 39 : 959 – 967 .
   PubMed Web of Science ®Google Scholar
• Evers , A and Klebe , G . 2004 . Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model . J. Med. Chem. , 47 : 5381 – 5392 .
   PubMed Web of Science ®Google Scholar
• Evers , A , Gohlke , H and Klebe , G . 2003 . Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials . J. Mol. Biol. , 334 : 327 – 345 .
   PubMed Web of Science ®Google Scholar
• www.chemcomp.com (www.chemcomp.com)
   Google Scholar
• Sheik , SS . 2002 . Ramachandran plot on the web . Bioinformatics , 18 : 1548 – 1549 .
   Google Scholar
• Verdonk , ML . 2003 . Improved protein-ligand docking using GOLD . Proteins , 52 : 609 – 623 .
   PubMed Web of Science ®Google Scholar
• Jones , G . 1997 . Development and validation of a genetic algorithm for flexible docking . J. Mol. Biol. , 267 : 727 – 748 .
   PubMed Web of Science ®Google Scholar
• Patny , A . 2006 . Ligand-supported homology modeling of the human angiotensin II type 1 (AT(1)) receptor: insights into the molecular determinants of telmisartan binding . Proteins: Structure, Function, and Bioinformatics , 65 : 824 – 842 .
   Google Scholar
• et , SRKimura . Systematic active site refinement of GPCR models through molecular dynamics simulation . Abstracts of paper presented at 231st ACS National Meeting . March 26–30 . Atlanta, GA, , United States (2006: COMP-218)
   Google Scholar
• Marinella , G . 2003 . Synthesis and pharmacological identification of neutral histamine H1-receptor antagonists . J. Med. Chem. , 46 : 5812 – 5824 .
   Google Scholar
• ter Laak , AM . 1995 . Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation . J. Comput. Aided Mol. Des. , 9 : 319 – 330 .
   PubMed Web of Science ®Google Scholar
• Wieland , K . 1999 . Mutational analysis of the antagonist-binding site of the histamine H(1) receptor . J. Biol. Chem. , 274 : 29994 – 30000 .
   PubMed Web of Science ®Google Scholar
• Ohta , K . 1994 . Site-directed mutagenesis of the histamine H1 receptor: roles ofaspartic acid107, asparagine198 and threonine194 . Biochem. Biophys. Res. Commun. , 203 : 1096 – 1101 .
   PubMed Web of Science ®Google Scholar
• http://protein.cribi.unipd.it/homer/ (http://protein.cribi.unipd.it/homer/)
   Google Scholar
• Tosatto , SCE . 2002 . A divide and conquer approach to fast, loop modeling . Protein Engg. , 15 : 279 – 286 .
   PubMedGoogle Scholar
• Canutescu , A , Shelenkov , AA and Dunbrack , RL Jr . 2003 . A graph theory algorithm for protein side-chain prediction . Protein Sci. , 12 : 2001 – 2014 .
   PubMed Web of Science ®Google Scholar
• Vriend , G . 1990 . WHAT IF: a molecular modeling and drug design program . J. Mol. Graph. , 8 : 52 – 56 .
   PubMed Web of Science ®Google Scholar
• Ahn , HS . 1999 . Structure-activity relationships of pyrroloquinazolines as thrombin receptor antagonists . Bioorg. Med. Chem. Lett. , 9 : 2073 – 2078 .
   Google Scholar
• Dixit , A . 2004 . Development of CoMFA, advance CoMFA and CoMSIA models in pyrroloquinazolines as thrombin receptor antagonist . Bioorg. Med. Chem. , 12 : 3591 – 3598 .
   PubMed Web of Science ®Google Scholar
• Zhang , HC . 2003 . High-affinity thrombin receptor (PAR-1) ligands: a new generation of indole-based peptide mimetic antagonists with a basic amine at the C-terminus . Bioorg. Med. Chem. Lett. , 13 : 2199 – 2203 .
   PubMedGoogle Scholar