chemogenomics references

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[Balakin2002Property-based] K. V. Balakin, S. E. Tkachenko, S. A. Lang, I. Okun, A. A. Ivashchenko, and N. P. Savchuk. Property-based design of GPCR-targeted library. J. Chem. Inf. Comput. Sci., 42(6):1332-1342, 2002. [ bib | Abstract ]
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[Bissantz2003Protein-based] C. Bissantz, P. Bernard, M. Hibert, and D. Rognan. Protein-based virtual screening of chemical databases. II. are homology models of G-protein coupled receptors suitable targets? Proteins, 50(1):5-25, Jan 2003. [ bib | DOI | http | Abstract ]
[Cavasotto2003Structure-based] C. N. Cavasotto, A. J. W. Orry, and R. A. Abagyan. Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins, 51(3):423-433, May 2003. [ bib | DOI | http | Abstract ]
[Shacham2004PREDICT] S. Shacham, Y. Marantz, S. Bar-Haim, O. Kalid, D. Warshaviak, N. Avisar, B. Inbal, A. Heifetz, M. Fichman, M. Topf, Z. Naor, S. Noiman, and O. M. Becker. PREDICT modeling and in-silico screening for G-protein coupled receptors. Proteins, 57(1):51-86, Oct 2004. [ bib | DOI | http | Abstract ]
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[Okada2004retinal] T. Okada, M. Sugihara, A.-N. Bondar, M. Elstner, P. Entel, and V. Buss. The retinal conformation and its environment in rhodopsin in light of a new 2.2 a crystal structure. J. Mol. Biol., 342(2):571-583, Sep 2004. [ bib | DOI | http | Abstract ]
[Lin2004Orphan] S. H. S. Lin and O. Civelli. Orphan G protein-coupled receptors: targets for new therapeutic interventions. Ann. Med., 36(3):204-214, 2004. [ bib | DOI | http | Abstract ]
[Bredel2004Chemogenomics] M. Bredel and E. Jacoby. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet., 5(4):262-275, Apr 2004. [ bib | DOI | http | .pdf ]
[Becker2004G] O. M. Becker, Y. Marantz, S. Shacham, B. Inbal, A. Heifetz, O. Kalid, S. Bar-Haim, D. Warshaviak, M. Fichman, and S. Noiman. G protein-coupled receptors: in silico drug discovery in 3D. Proc. Natl. Acad. Sci. USA, 101(31):11304-11309, Aug 2004. [ bib | DOI | http | Abstract ]
[Rolland2005G-protein-coupled] C. Rolland, R. Gozalbes, A. Nicolaï, M.-F. Paugam, L. Coussy, F. Barbosa, D. Horvath, and F. Revah. G-protein-coupled receptor affinity prediction based on the use of a profiling dataset: Qsar design, synthesis, and experimental validation. J. Med. Chem., 48(21):6563-6574, Oct 2005. [ bib | DOI | http | Abstract ]
[Lapinsh2005Improved] M. Lapinsh, P. Prusis, S. Uhlén, and J. E. S. Wikberg. Improved approach for proteochemometrics modeling: application to organic compound-amine G protein-coupled receptor interactions. Bioinformatics, 21(23):4289-4296, Dec 2005. [ bib | DOI | http | Abstract ]
[Kratochwil2005automated] N. A. Kratochwil, P. Malherbe, L. Lindemann, M. Ebeling, M. C. Hoener, A. Mühlemann, R. H. P. Porter, M. Stahl, and P. R. Gerber. An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application. J. Chem. Inf. Model., 45(5):1324-1336, 2005. [ bib | DOI | http | .pdf | Abstract ]
[Frimurer2005physicogenetic] T. M. Frimurer, T. Ulven, C. E. Elling, L.-O. Gerlach, E. Kostenis, and T. Högberg. A physicogenetic method to assign ligand-binding relationships between 7tm receptors. Bioorg. Med. Chem. Lett., 15(16):3707-3712, Aug 2005. [ bib | DOI | http | .pdf | Abstract ]
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[Evers2005Structure-based] A. Evers and T. Klabunde. Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor. J. Med. Chem., 48(4):1088-1097, Feb 2005. [ bib | DOI | http | Abstract ]
[Bock2005Virtual] J. R. Bock and D. A. Gough. Virtual screen for ligands of orphan G protein-coupled receptors. J. Chem. Inform. Model., 45(5):1402-1414, 2005. [ bib | DOI | http | .pdf | Abstract ]
[Martin2005bioavailability] Y. C. Martin. A bioavailability score. J. Med. Chem., 48(9):3164-3170, May 2005. [ bib | DOI | http | Abstract ]
[2006Chemical] S. E. Jaroch and H. Weinmann, editors. Chemical Genomics: Small Molecule Probes to Study Cellular Function. Ernst Schering Research Foundation Workshop. Springer, Berlin, 2006. [ bib ]
[Yao2006Coupling] X. Yao, C. Parnot, X. Deupi, V. R. P. Ratnala, G. Swaminath, D. Farrens, and B. Kobilka. Coupling ligand structure to specific conformational switches in the beta2-adrenoceptor. Nat. Chem. Biol., 2(8):417-422, Aug 2006. [ bib | DOI | http | Abstract ]
[Okuno2006GLIDA] Y. Okuno, J. Yang, K. Taneishi, H. Yabuuchi, and G. Tsujimoto. GLIDA: GPCR-ligand database for chemical genomic drug discovery. Nucleic Acids Res., 34(Database issue):D673-D677, Jan 2006. [ bib | DOI | http | Abstract ]
[Klabunde2006Chemogenomics] T. Klabunde and R. Jäger. Chemogenomics approaches to g-protein coupled receptor lead finding. Ernst Schering Res Found Workshop, 58:31-46, 2006. [ bib | Abstract ]
[Hill2006G-protein-coupled] S. J. Hill. G-protein-coupled receptors: past, present and future. Br. J. Pharmacol., 147 Suppl 1:S27-S37, Jan 2006. [ bib | DOI | http | Abstract ]
[Guba2006Chemogenomics] W. Guba. Chemogenomics strategies for g-protein coupled receptor hit finding. Ernst Schering Res Found Workshop, 58:21-29, 2006. [ bib | DOI | Abstract ]
[Erhan2006Collaborative] D. Erhan, P.-J. L'heureux, S. Y. Yue, and Y. Bengio. Collaborative filtering on a family of biological targets. J. Chem. Inf. Model., 46(2):626-635, 2006. [ bib | DOI | http | .pdf | Abstract ]
[Okuno2007GLIDA] Y. Okuno, A. Tamon, H. Yabuuchi, S. Niijima, Y. Minowa, K. Tonomura, R. Kunimoto, and C. Feng. GLIDA: GPCR ligand database for chemical genomics drug discovery database and tools update. Nucleic Acids Res., 36(Database issue):D907-D912, Nov 2007. [ bib | DOI | http | Abstract ]
[Kobilka2007G] B. K. Kobilka. G protein coupled receptor structure and activation. Biochim. Biophys. Acta, 1768(4):794-807, Apr 2007. [ bib | DOI | http | Abstract ]
[Jacob2007Kernel] L. Jacob and J.-P. Vert. Kernel methods for in silico chemogenomics. Technical Report 0709.3931v1, arXiv, 2007. [ bib | http ]
[Deupi2007Structural] X. Deupi, N. Dölker, M. L. Lòpez-Rodrìguez, M. Campillo, J. A. Ballesteros, and L. Pardo. Structural models of class a G protein-coupled receptors as a tool for drug design: insights on transmembrane bundle plasticity. Curr. Top. Med. Chem., 7(10):991-998, 2007. [ bib | Abstract ]
[Chen2007GPCR] J.-Z. Chen, J. Wang, and X.-Q. Xie. Gpcr structure-based virtual screening approach for cb2 antagonist search. J. Chem. Inf. Model., 47(4):1626-1637, 2007. [ bib | DOI | http | .pdf | Abstract ]
[Catapano2007G] L. A. Catapano and H. K. Manji. G protein-coupled receptors in major psychiatric disorders. Biochim. Biophys. Acta, 1768(4):976-993, Apr 2007. [ bib | DOI | http ]
[Avlani2007Critical] V. A. Avlani, K. J. Gregory, C. J. Morton, M. W. Parker, P. M. Sexton, and A. Christopoulos. Critical role for the second extracellular loop in the binding of both orthosteric and allosteric g protein-coupled receptor ligands. J. Biol. Chem., 282(35):25677-25686, Aug 2007. [ bib | DOI | http | Abstract ]
[Klabunde2007Chemogenomic] T. Klabunde. Chemogenomic approaches to drug discovery: similar receptors bind similar ligands. Br. J. Pharmacol., 152:5-7, May 2007. [ bib | DOI | http | Abstract ]
[Fredholm2007G-protein-coupled] B. B. Fredholm, T. Hökfelt, and G. Milligan. G-protein-coupled receptors: an update. Acta Physiol., 190(1):3-7, May 2007. [ bib | DOI | http | Abstract ]
[Lefkowitz2008crystal] R. J. Lefkowitz, J.-P. Sun, and A. K. Shukla. A crystal clear view of the beta2-adrenergic receptor. Nat. Biotechnol., 26(2):189-191, Feb 2008. [ bib | DOI | http ]
[Kellenberger2008How] E. Kellenberger, C. Schalon, and D. Rognan. How to measure the similarity between protein ligand-binding sites? Current Computer-Aided Drug Design, 4(3):209-220, Sep. 2008. [ bib | DOI | http | .pdf | Abstract ]
[Jacob2008Protein] L. Jacob and J.-P. Vert. Protein-ligand interaction prediction: an improved chemogenomics approach. Bioinformatics, 24(19):2149-2156, 2008. [ bib | DOI | http | .pdf ]
[Jacob2008Efficient] L. Jacob and J.-P. Vert. Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics, 24(3):358-366, Feb 2008. [ bib | DOI | http | .pdf | Abstract ]
[Jacob2008Virtual] L. Jacob, B. Hoffmann, V. Stoven, and J.-P. Vert. Virtual screening of GPCRs: an in silico chemogenomics approach. BMC Bioinformatics, 9:363, 2008. [ bib | DOI | http | .pdf ]
[Cavasotto2008Discovery] C. N. Cavasotto, A. J. W. Orry, N. J. Murgolo, M. F. Czarniecki, S. A. Kocsi, B. E. Hawes, K. A. O'Neill, H. Hine, M. S. Burton, J. H. Voigt, R. A. Abagyan, M. L. Bayne, and F. J. Monsma. Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J. Med. Chem., 51(3):581-588, Feb 2008. [ bib | DOI | http | Abstract ]
[Wassermann2009Ligand] Anne Mai Wassermann, Hanna Geppert, and Jürgen Bajorath. Ligand prediction for orphan targets using support vector machines and various target-ligand kernels is dominated by nearest neighbor effects. J Chem Inf Model, 49(10):2155-2167, Oct 2009. [ bib | DOI | http | .pdf | Abstract ]
[Shivakumar2009Structural] Pavithra Shivakumar and Michael Krauthammer. Structural similarity assessment for drug sensitivity prediction in cancer. BMC Bioinformatics, 10 Suppl 9:S17, 2009. [ bib | DOI | http | .pdf | Abstract ]

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