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Volumn 54, Issue 8, 2014, Pages 2261-2274

Benchmark data sets for structure-based computational target prediction

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING; LIGANDS; PROTEINS;

EID: 84906568966     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500131x     Document Type: Article
Times cited : (18)

References (50)
  • 1
    • 33846518797 scopus 로고    scopus 로고
    • In silico target fishing: Predicting biological targets from chemical structure
    • Jenkins, J. L.; Bender, A.; Davied, J. W. In silico target fishing: Predicting biological targets from chemical structure Drug Discovery Today 2006, 3 (4) 413-421
    • (2006) Drug Discovery Today , vol.3 , Issue.4 , pp. 413-421
    • Jenkins, J.L.1    Bender, A.2    Davied, J.W.3
  • 2
    • 34548319111 scopus 로고    scopus 로고
    • In silico pharmacology for drug discovery applications to targets and beyond
    • Ekins, S.; Mesters, J.; Testa, B. In silico pharmacology for drug discovery applications to targets and beyond Br. J. Pharmacol. 2007, 152, 21-37
    • (2007) Br. J. Pharmacol. , vol.152 , pp. 21-37
    • Ekins, S.1    Mesters, J.2    Testa, B.3
  • 3
    • 34548317031 scopus 로고    scopus 로고
    • Chemogenomic approaches to rational drug design
    • Rognan, D. Chemogenomic approaches to rational drug design Br. J. Pharmacol. 2007, 152, 38-52
    • (2007) Br. J. Pharmacol. , vol.152 , pp. 38-52
    • Rognan, D.1
  • 4
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins, A. L. Network pharmacology: The next paradigm in drug discovery Nat. Chem. Biol. 2008, 4 (11) 682-690
    • (2008) Nat. Chem. Biol. , vol.4 , Issue.11 , pp. 682-690
    • Hopkins, A.L.1
  • 5
    • 77952683248 scopus 로고    scopus 로고
    • Structure-based approaches to target fishing and ligand profiling
    • Rognan, D. Structure-based approaches to target fishing and ligand profiling Mol. Inf. 2010, 29, 176-187
    • (2010) Mol. Inf. , vol.29 , pp. 176-187
    • Rognan, D.1
  • 6
    • 84875150414 scopus 로고    scopus 로고
    • The holistic integration of virtual screening in drug discovery
    • Tanrikulu, Y.; Krüger, B.; Proschak, E. The holistic integration of virtual screening in drug discovery Drug Discovery Today 2013, 18, 358-364
    • (2013) Drug Discovery Today , vol.18 , pp. 358-364
    • Tanrikulu, Y.1    Krüger, B.2    Proschak, E.3
  • 7
    • 77952683248 scopus 로고    scopus 로고
    • Structure-based approaches to target fishing and ligand profiling
    • Rognan, D. Structure-based approaches to target fishing and ligand profiling Mol. Inf. 2010, 29, 176-187
    • (2010) Mol. Inf. , vol.29 , pp. 176-187
    • Rognan, D.1
  • 9
    • 41349106542 scopus 로고    scopus 로고
    • Recommendations for evaluation of computational methods
    • Jain, A. N.; Nicholls, A. Recommendations for evaluation of computational methods J. Comput.-Aided Mol. Des. 2008, 22, 133-139
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 133-139
    • Jain, A.N.1    Nicholls, A.2
  • 10
    • 34247272948 scopus 로고    scopus 로고
    • Evaluating virtual screening methods: Good and bad metrics for the early recognition" problem
    • Truchon, J.-F.; Bayly, C. I. Evaluating virtual screening methods: Good and bad metrics for the early recognition" problem J. Chem. Inf. Model. 2007, 47, 488-508
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 488-508
    • Truchon, J.-F.1    Bayly, C.I.2
  • 11
    • 41349106585 scopus 로고    scopus 로고
    • Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-What can we learn from earlier mistakes?
    • Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-What can we learn from earlier mistakes? J. Comput.-Aided Mol. Des. 2008, 22, 213-228
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 213-228
    • Kirchmair, J.1    Markt, P.2    Distinto, S.3    Wolber, G.4    Langer, T.5
  • 12
    • 0035217619 scopus 로고    scopus 로고
    • Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach
    • Chen, Y. Z.; Ung, C. Y. Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach J. Mol. Graph. Model. 2001, 20 (3) 199-218
    • (2001) J. Mol. Graph. Model. , vol.20 , Issue.3 , pp. 199-218
    • Chen, Y.Z.1    Ung, C.Y.2
  • 13
    • 0035342428 scopus 로고    scopus 로고
    • Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
    • Chen, Y. Z.; Zhi, D. G. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule Proteins 2001, 43 (2) 217-226
    • (2001) Proteins , vol.43 , Issue.2 , pp. 217-226
    • Chen, Y.Z.1    Zhi, D.G.2
  • 16
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49 (23) 6789-6801
    • (2006) J. Med. Chem. , vol.49 , Issue.23 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 17
    • 84883239935 scopus 로고    scopus 로고
    • In silico target predictions: Defining a benchmarking dataset and comparison of performance of the multiclass naïve bayes and Parzen-Rosenblatt window
    • Koutsoukas, A.; Lowe, R.; KalantarMotamedi, Y.; Mussa, H. Y.; Klaffke, W.; Mitchell, J. B. O.; Glen, R. C.; Bender, A. In silico target predictions: Defining a benchmarking dataset and comparison of performance of the multiclass naïve bayes and Parzen-Rosenblatt window J. Chem. Inf. Model. 2013, 53 (8) 1957-1966
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.8 , pp. 1957-1966
    • Koutsoukas, A.1    Lowe, R.2    Kalantarmotamedi, Y.3    Mussa, H.Y.4    Klaffke, W.5    Mitchell, J.B.O.6    Glen, R.C.7    Bender, A.8
  • 18
    • 1542286205 scopus 로고    scopus 로고
    • Recovering the true targets of specific ligands by virtual screening of the protein data bank
    • Paul, N.; Kellenberger, E.; Bret, G.; Müller, P.; Rognan, D. Recovering the true targets of specific ligands by virtual screening of the protein data bank Proteins. 2004, 54 (4) 671-680
    • (2004) Proteins. , vol.54 , Issue.4 , pp. 671-680
    • Paul, N.1    Kellenberger, E.2    Bret, G.3    Müller, P.4    Rognan, D.5
  • 19
    • 45749117025 scopus 로고    scopus 로고
    • Ranking targets in structure-based virtual screening of three-dimensional protein libraries: Methods and problems
    • Kellenberger, E.; Foata, N.; Rognan, D. Ranking targets in structure-based virtual screening of three-dimensional protein libraries: methods and problems J. Chem. Inf. Model. 2008, 48 (5) 1014-1025
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.5 , pp. 1014-1025
    • Kellenberger, E.1    Foata, N.2    Rognan, D.3
  • 20
    • 84862011491 scopus 로고    scopus 로고
    • Protein-ligand-based pharmacophores: Generation and utility assessment in computational ligand profiling
    • Meslamani, J.; Li, J.; Sutter, J.; Stevens, A.; Bertrand, H.-O.; Rognan, D. Protein-ligand-based pharmacophores: Generation and utility assessment in computational ligand profiling J. Chem. Inf. Model. 2012, 52 (4) 943-955
    • (2012) J. Chem. Inf. Model. , vol.52 , Issue.4 , pp. 943-955
    • Meslamani, J.1    Li, J.2    Sutter, J.3    Stevens, A.4    Bertrand, H.-O.5    Rognan, D.6
  • 21
    • 79954520873 scopus 로고    scopus 로고
    • Sc-PDB: A database for identifying variations and multiplicity of 'druggable' binding sites in proteins
    • Meslamani, J.; Rognan, D.; Kellenberger, E. sc-PDB: A database for identifying variations and multiplicity of 'druggable' binding sites in proteins Bioinformatics. 2011, 27 (9) 1324-1326
    • (2011) Bioinformatics. , vol.27 , Issue.9 , pp. 1324-1326
    • Meslamani, J.1    Rognan, D.2    Kellenberger, E.3
  • 22
    • 84903286855 scopus 로고    scopus 로고
    • Facing the challenges of structure-based target prediction by inverse virtual screening
    • Schomburg, K. T.; Bietz, S.; Briem, H.; Henzler, A.; Urbaczek, S.; Rarey, M. Facing the challenges of structure-based target prediction by inverse virtual screening J. Chem. Inf. Model. 2014, 54, 1676-1686
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1676-1686
    • Schomburg, K.T.1    Bietz, S.2    Briem, H.3    Henzler, A.4    Urbaczek, S.5    Rarey, M.6
  • 23
    • 33947119575 scopus 로고    scopus 로고
    • Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pka calculations and itc experiments
    • Czodrowski, P.; Sotriffer, P. A.; Klebe, G. Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pka calculations and itc experiments J. Mol. Biol. 2007, 367 (5) 1347-1356
    • (2007) J. Mol. Biol. , vol.367 , Issue.5 , pp. 1347-1356
    • Czodrowski, P.1    Sotriffer, P.A.2    Klebe, G.3
  • 24
    • 41849107110 scopus 로고    scopus 로고
    • Understanding binding selectivity toward trypsin and factor Xa: The role of aromatic interactions
    • Di Fenza, A.; Heine, A.; Koert, U.; Klebe, G. Understanding binding selectivity toward trypsin and factor Xa: The role of aromatic interactions ChemMedChem. 2007, 2 (3) 297-308
    • (2007) ChemMedChem. , vol.2 , Issue.3 , pp. 297-308
    • Di Fenza, A.1    Heine, A.2    Koert, U.3    Klebe, G.4
  • 25
  • 26
    • 84883220985 scopus 로고    scopus 로고
    • Cavities tell more than sequences: Exploring functional relationships of proteases via binding pockets
    • Glinca, S.; Klebe, G. Cavities tell more than sequences: Exploring functional relationships of proteases via binding pockets J. Chem. Inf. Model. 2013, 53 (8) 2082-2092
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.8 , pp. 2082-2092
    • Glinca, S.1    Klebe, G.2
  • 27
    • 52949140176 scopus 로고    scopus 로고
    • PDE4 inhibitors: Current status
    • Spina, D. PDE4 inhibitors: Current status Br. J. Pharmacol. 2008, 155 (3) 308-315
    • (2008) Br. J. Pharmacol. , vol.155 , Issue.3 , pp. 308-315
    • Spina, D.1
  • 28
    • 33746154470 scopus 로고    scopus 로고
    • Comparison of phosphodiesterase type 5 (PDE5) inhibitors
    • Wright, P. J. Comparison of phosphodiesterase type 5 (PDE5) inhibitors Int. J. Clin. Pract. 2006, 60 (8) 967-975
    • (2006) Int. J. Clin. Pract. , vol.60 , Issue.8 , pp. 967-975
    • Wright, P.J.1
  • 29
    • 36048958965 scopus 로고    scopus 로고
    • Histone deacetylase inhibitors: Overview and perspectives
    • Dokmanovic, M.; Clarke, C.; Marks, P. A. Histone deacetylase inhibitors: Overview and perspectives Mol. Cancer Res. 2007, 5 (10) 981-989
    • (2007) Mol. Cancer Res. , vol.5 , Issue.10 , pp. 981-989
    • Dokmanovic, M.1    Clarke, C.2    Marks, P.A.3
  • 33
    • 54949108677 scopus 로고    scopus 로고
    • Pubchem: Integrated platform of small molecules and biological activities
    • Bolton, E. E.; Wang, Y.; Thiessen, P. A.; Bryant, S. H. Pubchem: Integrated platform of small molecules and biological activities Annu. Rep. Comput. Chem. 2008, 4, 217-241
    • (2008) Annu. Rep. Comput. Chem. , vol.4 , pp. 217-241
    • Bolton, E.E.1    Wang, Y.2    Thiessen, P.A.3    Bryant, S.H.4
  • 34
    • 84906564509 scopus 로고    scopus 로고
    • (accessed January)
    • ftp://cheminfo.u-strasbg.fr (accessed January 2013).
    • (2013)
  • 37
    • 77952772341 scopus 로고    scopus 로고
    • Extended-connectivity fingerprints
    • Rogers, D.; Hahn, M. Extended-connectivity fingerprints J. Chem. Inf. Model. 2010, 50 (5) 742-754
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.5 , pp. 742-754
    • Rogers, D.1    Hahn, M.2
  • 39
    • 78650689245 scopus 로고    scopus 로고
    • Comprehensive comparison of ligand-based virtual screening tools against the DUD dataset reveals limitations of current 3D methods
    • Venkatraman, V.; Pérez-Nueno, V.; Mavridis, L.; Ritchie, D. W. Comprehensive comparison of ligand-based virtual screening tools against the DUD dataset reveals limitations of current 3D methods J. Chem. Inf. Model. 2010, 50, 2079-2093
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2079-2093
    • Venkatraman, V.1    Pérez-Nueno, V.2    Mavridis, L.3    Ritchie, D.W.4
  • 40
    • 84879897900 scopus 로고    scopus 로고
    • Open-source platform to benchmark fingerprints for ligand-based virtual screening
    • Riniker, S.; Landrum, G. A. Open-source platform to benchmark fingerprints for ligand-based virtual screening J. Cheminform. 2013, 5, 26
    • (2013) J. Cheminform. , vol.5 , pp. 26
    • Riniker, S.1    Landrum, G.A.2
  • 41
    • 66149105428 scopus 로고    scopus 로고
    • Beyond the virtual screening paradigm: Structure-based searching for new lead compounds
    • Schlosser, J.; Rarey, M. Beyond the virtual screening paradigm: Structure-based searching for new lead compounds J. Chem. Inf. Model. 2009, 49, 800-809
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 800-809
    • Schlosser, J.1    Rarey, M.2
  • 44
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne, M. J.; Schnell, J.; Benkovic, S. J.; Dyson, H. J.; Wright, P. E. Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism Biochemistry. 2001, 40 (33) 9846-9859
    • (2001) Biochemistry. , vol.40 , Issue.33 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 45
    • 0029775802 scopus 로고    scopus 로고
    • Down-regulation of the mineralocorticoid receptor by dexamethasone in an amphibian kidney cell line (A6)
    • Hagley, R. D.; Watlington, C. O. Down-regulation of the mineralocorticoid receptor by dexamethasone in an amphibian kidney cell line (A6) Endocr. Res. 1996, 22 (3) 221-235
    • (1996) Endocr. Res. , vol.22 , Issue.3 , pp. 221-235
    • Hagley, R.D.1    Watlington, C.O.2
  • 50
    • 84984554819 scopus 로고    scopus 로고
    • Comparative study of the inhibitory effect of antidepressants on cholinesterase activity in Bungarussindanus (krait) venom, human serum and rat striatum
    • Ahmed, M.; Rocha, J. B. T.; Mazzanti, C. M.; Hassan, W.; Morsch, V. M.; Loro, V. L.; Thome, G.; Schetinger, M.R. C. Comparative study of the inhibitory effect of antidepressants on cholinesterase activity in Bungarussindanus (krait) venom, human serum and rat striatum J. Enzyme Inhib. Med. Chem. 2008, 23 (6) 912-917
    • (2008) J. Enzyme Inhib. Med. Chem. , vol.23 , Issue.6 , pp. 912-917
    • Ahmed, M.1    Rocha, J.B.T.2    Mazzanti, C.M.3    Hassan, W.4    Morsch, V.M.5    Loro, V.L.6    Thome, G.7    Schetinger, M.R.C.8


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