메뉴 건너뛰기




Volumn 48, Issue 4, 2008, Pages 704-718

Impact of benchmark data set topology on the validation of virtual screening methods: Exploration and quantification by spatial statistics

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARKING; LIGANDS; STATISTICAL METHODS; SYSTEMS ANALYSIS;

EID: 44449122375     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700099u     Document Type: Article
Times cited : (31)

References (63)
  • 2
    • 15544365691 scopus 로고    scopus 로고
    • New methodologies for ligand-based virtual screening
    • Stahura, F. L.; Bajorath, J. New methodologies for ligand-based virtual screening. Curr. Pharm. Des. 2005, 11, 1189-1202.
    • (2005) Curr. Pharm. Des , vol.11 , pp. 1189-1202
    • Stahura, F.L.1    Bajorath, J.2
  • 3
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug. Discov. 2004, 3, 935-949.
    • (2004) Nat. Rev. Drug. Discov , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 4
    • 0029783934 scopus 로고    scopus 로고
    • Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors
    • Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors. J. Med. Chem. 1996, 39, 3049-3059.
    • (1996) J. Med. Chem , vol.39 , pp. 3049-3059
    • Patterson, D.E.1    Cramer, R.D.2    Ferguson, A.M.3    Clark, R.D.4    Weinberger, L.E.5
  • 5
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity
    • Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity. J. Med. Chem. 2002, 45, 4350-4358.
    • (2002) J. Med. Chem , vol.45 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 7
    • 0342645323 scopus 로고    scopus 로고
    • Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection
    • Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
    • (1996) J. Chem. Inf. Comput. Sci , vol.36 , pp. 572-584
    • Brown, R.D.1    Martin, Y.C.2
  • 8
    • 5244364312 scopus 로고    scopus 로고
    • The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding
    • Brown, R. D.; Martin, Y. C. The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 1997, 37, 1-9.
    • (1997) J. Chem. Inf. Comput. Sci , vol.37 , pp. 1-9
    • Brown, R.D.1    Martin, Y.C.2
  • 10
    • 10244222365 scopus 로고    scopus 로고
    • Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
    • Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org. Biomol. Chem. 2004, 2, 3256-3266.
    • (2004) Org. Biomol. Chem , vol.2 , pp. 3256-3266
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 11
    • 0035865781 scopus 로고    scopus 로고
    • Improved Scoring of Ligand-Protein Interactions Using OWFEG Free Energy Grids
    • Pearlman, D. A.; Charifson, P. S. Improved Scoring of Ligand-Protein Interactions Using OWFEG Free Energy Grids. J. Med. Chem. 2001, 44, 502-511.
    • (2001) J. Med. Chem , vol.44 , pp. 502-511
    • Pearlman, D.A.1    Charifson, P.S.2
  • 12
    • 26944443036 scopus 로고    scopus 로고
    • A discussion of measures of enrichment in virtual screening: Comparing the information content of descriptors with increasing levels of sophistication
    • Bender, A.; Glen, R. C. A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication. J. Chem. Inf. Model. 2005, 45, 1369-1375.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1369-1375
    • Bender, A.1    Glen, R.C.2
  • 13
    • 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
  • 14
    • 0035438401 scopus 로고    scopus 로고
    • Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches
    • Sheridan, R. P.; Singh, S. B.; Fluder, E. M.; Kearsley, S. K. Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches. J. Chem. Inf. Model. 2001, 41, 1395-1406.
    • (2001) J. Chem. Inf. Model , vol.41 , pp. 1395-1406
    • Sheridan, R.P.1    Singh, S.B.2    Fluder, E.M.3    Kearsley, S.K.4
  • 15
    • 33646730764 scopus 로고    scopus 로고
    • Robust Ligand-Based Modeling of the Biological Targets of Known Drugs
    • Cleves, A. E.; Jain, A. N. Robust Ligand-Based Modeling of the Biological Targets of Known Drugs. J. Med. Chem. 2006, 49, 2921-2938.
    • (2006) J. Med. Chem , vol.49 , pp. 2921-2938
    • Cleves, A.E.1    Jain, A.N.2
  • 16
    • 33646740651 scopus 로고    scopus 로고
    • Parameter Estimation for Scoring Protein-Ligand Interactions Using Negative Training Data
    • Pham, T. A.; Jain, A. N. Parameter Estimation for Scoring Protein-Ligand Interactions Using Negative Training Data. J. Med. Chem. 2006, 49, 5856-5868.
    • (2006) J. Med. Chem , vol.49 , pp. 5856-5868
    • Pham, T.A.1    Jain, A.N.2
  • 17
    • 10044254671 scopus 로고    scopus 로고
    • Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease
    • Klon, A. E.; Glick, M.; Davies, J. W. Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease. J. Chem. Inf. Model. 2004, 44, 2216-2224.
    • (2004) J. Chem. Inf. Model , vol.44 , pp. 2216-2224
    • Klon, A.E.1    Glick, M.2    Davies, J.W.3
  • 18
    • 17144385534 scopus 로고    scopus 로고
    • Virtual Screening Workflow Development Guided by the "Receiver Operating Characteristic" Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4
    • Triballeau, N.; Acher, F.; Brabet, I.; Pin, J. P.; Bertrand, H. O. Virtual Screening Workflow Development Guided by the "Receiver Operating Characteristic" Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4. J. Med. Chem. 2005, 48, 2534-2547.
    • (2005) J. Med. Chem , vol.48 , pp. 2534-2547
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.P.4    Bertrand, H.O.5
  • 19
    • 44449118958 scopus 로고    scopus 로고
    • Elsevier MDL: San Ramon, CA
    • MDL Drug Data Report (MDDR); Elsevier MDL: San Ramon, CA, 2005.
    • (2005) MDL Drug Data Report (MDDR)
  • 20
    • 33646270382 scopus 로고    scopus 로고
    • Training similarity measures for specific activities: Application to reduced graphs
    • Birchall, K.; Gillet, V. J.; Harper, G.; Pickett, S. D. Training similarity measures for specific activities: application to reduced graphs. J. Chem. Inf. Model. 2006, 46, 577-586.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 577-586
    • Birchall, K.1    Gillet, V.J.2    Harper, G.3    Pickett, S.D.4
  • 23
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
    • Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-4767.
    • (2000) J. Med. Chem , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 24
    • 23844555629 scopus 로고    scopus 로고
    • Consensus Scoring Criteria for Improving Enrichment in Virtual Screening
    • Yang, J.-M.; Chen, Y.-F.; Shen, T.-W.; Kristal, B.; Hsu, D. Consensus Scoring Criteria for Improving Enrichment in Virtual Screening. J. Chem. Inf. Model. 2005, 45, 1134-1146.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1134-1146
    • Yang, J.-M.1    Chen, Y.-F.2    Shen, T.-W.3    Kristal, B.4    Hsu, D.5
  • 25
    • 5544290537 scopus 로고    scopus 로고
    • Similarity searching of chemical databases using atom environment descriptors (MOL-PRINT 2D): Evaluation of performance
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors (MOL-PRINT 2D): evaluation of performance. J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 1708-1718
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3    Reiling, S.4
  • 26
    • 10044265608 scopus 로고    scopus 로고
    • The reduced graph descriptor in virtual screening and data-driven clustering of high-throughput screening data
    • Harper, G.; Bravi, G. S.; Pickett, S. D.; Hussain, J.; Green, D. V. S. The reduced graph descriptor in virtual screening and data-driven clustering of high-throughput screening data. J. Chem. Inf. Comput. Sci. 2004, 44, 2145-2156.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 2145-2156
    • Harper, G.1    Bravi, G.S.2    Pickett, S.D.3    Hussain, J.4    Green, D.V.S.5
  • 27
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 1995, 245, 43-53.
    • (1995) J. Mol. Biol , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 28
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • 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.
    • (1997) J. Mol. Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 30
    • 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, 6789-6801.
    • (2006) J. Med. Chem , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 31
    • 20844436604 scopus 로고    scopus 로고
    • Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
    • Good, A. C.; Hermsmeier, M. A.; Hindle, S. A. Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments. J. Comput.-Aided. Mol. Des. 2004, 18, 529-536.
    • (2004) J. Comput.-Aided. Mol. Des , vol.18 , pp. 529-536
    • Good, A.C.1    Hermsmeier, M.A.2    Hindle, S.A.3
  • 32
    • 33846856722 scopus 로고    scopus 로고
    • Measuring CAMD technique performance. 2. How "druglike" are drugs? Implications of Random test set selection exemplified using druglikeness classification models
    • Good, A. C.; Hermsmeier, M. A. Measuring CAMD technique performance. 2. How "druglike" are drugs? Implications of Random test set selection exemplified using druglikeness classification models. J. Chem. Inf. Model. 2007, 47, 110-114.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 110-114
    • Good, A.C.1    Hermsmeier, M.A.2
  • 33
    • 34247216044 scopus 로고    scopus 로고
    • Introduction of an information-theoretic method to predict recovery rates of active compounds for Bayesian in silico screening: Theory and screening trials
    • Vogt, M.; Bajorath, J. Introduction of an information-theoretic method to predict recovery rates of active compounds for Bayesian in silico screening: theory and screening trials. J. Chem. Inf. Model. 2007, 47, 337-341.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 337-341
    • Vogt, M.1    Bajorath, J.2
  • 34
    • 37849012382 scopus 로고    scopus 로고
    • Introduction of a Generally Applicable Method to Estimate Retrieval of Active Molecules for Similarity Searching using Fingerprints
    • Vogt, M.; Bajorath, J. Introduction of a Generally Applicable Method to Estimate Retrieval of Active Molecules for Similarity Searching using Fingerprints. ChemMedChem 2007, 2, 1311-1320.
    • (2007) ChemMedChem , vol.2 , pp. 1311-1320
    • Vogt, M.1    Bajorath, J.2
  • 36
    • 0002766180 scopus 로고
    • Statistical methods for spatial point patterns in ecology
    • Cormack, R. M, Ord, J. K, Eds, International Cooperative Publishing House: Fairland, MD
    • Diggle, P. J. Statistical methods for spatial point patterns in ecology. In Spatial and temporal analysis in ecology; Cormack, R. M., Ord, J. K., Eds.; International Cooperative Publishing House: Fairland, MD, 1979; pp 95-150.
    • (1979) Spatial and temporal analysis in ecology , pp. 95-150
    • Diggle, P.J.1
  • 37
    • 0342645331 scopus 로고    scopus 로고
    • 03; Chemical Computing Group, Inc, Montreal, Canada
    • MOE Molecular Operating Environment, 2002.03; Chemical Computing Group, Inc.: Montreal, Canada, 2002.
    • (2002) MOE Molecular Operating Environment
  • 38
    • 40949156290 scopus 로고    scopus 로고
    • Elsevier MDL: San Ramon, CA
    • CTFile Formats; Elsevier MDL: San Ramon, CA, 2005.
    • (2005) CTFile Formats
  • 41
    • 44449145986 scopus 로고    scopus 로고
    • 2.2; OpenEye Scientific Software, Inc, Santa Fe, NM
    • BABELS, 2.2; OpenEye Scientific Software, Inc.: Santa Fe, NM, 2006.
    • (2006) BABELS
  • 42
    • 44449136015 scopus 로고    scopus 로고
    • 2.0.1; OpenEye Scientific Software, Inc, Santa Fe, NM
    • FILTER, 2.0.1; OpenEye Scientific Software, Inc.: Santa Fe, NM, 2007.
    • (2007) FILTER
  • 44
    • 0020799674 scopus 로고
    • Some guidelines for constructing exact D-optimal designs on convex design spaces
    • Johnson, M. E.; Nachtsheim, C. J. Some guidelines for constructing exact D-optimal designs on convex design spaces. Technometrics 1983, 25, 271-277.
    • (1983) Technometrics , vol.25 , pp. 271-277
    • Johnson, M.E.1    Nachtsheim, C.J.2
  • 46
    • 20444476513 scopus 로고    scopus 로고
    • Controlling coverage of D-optimal onion designs and selections
    • Olsson, I. M.; Gottfries, J.; Wold, S. Controlling coverage of D-optimal onion designs and selections. J. Chemom. 2004, 18, 548-557.
    • (2004) J. Chemom , vol.18 , pp. 548-557
    • Olsson, I.M.1    Gottfries, J.2    Wold, S.3
  • 47
    • 0020876960 scopus 로고    scopus 로고
    • Scott, D. W.; Thompson, J. R. Probability density estimation in higher dimensions, In Interface: Computer Science and Statistics; Proceedings of the Fifteenth Symposium, Houston, TX, 1983; Gentle, J., Ed.; North-Holland: Amsterdam, The Netherlands, 1983; pp 173-179.
    • Scott, D. W.; Thompson, J. R. Probability density estimation in higher dimensions, In Interface: Computer Science and Statistics; Proceedings of the Fifteenth Symposium, Houston, TX, 1983; Gentle, J., Ed.; North-Holland: Amsterdam, The Netherlands, 1983; pp 173-179.
  • 48
    • 0003994186 scopus 로고    scopus 로고
    • Matlab 7;, Natick, MA
    • Matlab 7; The Mathworks: Natick, MA, 2006.
    • (2006) The Mathworks
  • 51
    • 33745343573 scopus 로고    scopus 로고
    • A distance function for retrieval of active molecules from complex chemical space representations
    • Godden, J. W.; Bajorath, J. A distance function for retrieval of active molecules from complex chemical space representations. J. Chem. Inf. Model. 2006, 46, 1094-1097.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1094-1097
    • Godden, J.W.1    Bajorath, J.2
  • 52
    • 33646228824 scopus 로고    scopus 로고
    • Kellenberger, E.; Muller, P.; Schalon, C.; Bret, G.; Foata, N.; Rognan, D. sc-PDB: an annotated database of draggable binding sites from the Protein Data Bank. J. Chem. Inf. Model. 2006, 46, 717-727.
    • Kellenberger, E.; Muller, P.; Schalon, C.; Bret, G.; Foata, N.; Rognan, D. sc-PDB: an annotated database of draggable binding sites from the Protein Data Bank. J. Chem. Inf. Model. 2006, 46, 717-727.
  • 53
    • 0037020329 scopus 로고    scopus 로고
    • Drug design strategies for targeting G-protein-coupled receptors
    • Klabunde, T.; Hessler, G. Drug design strategies for targeting G-protein-coupled receptors. ChemBioChem. 2002, 3, 928-944.
    • (2002) ChemBioChem , vol.3 , pp. 928-944
    • Klabunde, T.1    Hessler, G.2
  • 54
    • 44449170390 scopus 로고    scopus 로고
    • Ripley, B. D. 2nd-Order analysis of stationary point processes. J. Appl. Probab. 1976, 13, 255-266.
    • Ripley, B. D. 2nd-Order analysis of stationary point processes. J. Appl. Probab. 1976, 13, 255-266.
  • 55
    • 33746932104 scopus 로고    scopus 로고
    • R-NN curves: An intuitive approach to outlier detection using a distance based method
    • Guha, R.; Dutta, D.; Jurs, P. C.; Chen, T. R-NN curves: an intuitive approach to outlier detection using a distance based method. J. Chem. Inf. Model. 2006, 46, 1713-22.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1713-1722
    • Guha, R.1    Dutta, D.2    Jurs, P.C.3    Chen, T.4
  • 59
    • 0003410791 scopus 로고    scopus 로고
    • Springer-Verlag New York, Inc, Secaucus, NJ
    • Kohonen, T. Self-organizing maps; Springer-Verlag New York, Inc.: Secaucus, NJ, 1997.
    • (1997) Self-organizing maps
    • Kohonen, T.1
  • 61
    • 38049168357 scopus 로고    scopus 로고
    • SOM-Based Data Visualization Methods
    • Vesanto, J. SOM-Based Data Visualization Methods. Intell. Data Anal. 1999, 2, 111-126.
    • (1999) Intell. Data Anal , vol.2 , pp. 111-126
    • Vesanto, J.1
  • 63
    • 44449120322 scopus 로고    scopus 로고
    • Alhoniemi, E.; Himberg, J.; Parhankangas, J.; Vesanto, J. SOM Toolbox, 2.0; SOM Toolbox Team, Laboratory of Computer and Information Science: Helsinki, Finland, 2005.
    • Alhoniemi, E.; Himberg, J.; Parhankangas, J.; Vesanto, J. SOM Toolbox, 2.0; SOM Toolbox Team, Laboratory of Computer and Information Science: Helsinki, Finland, 2005.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.