Knowledge-based interaction fingerprint scoring: A simple method for improving the effectiveness of fast scoring functions

Journal of Chemical Information and Modeling

Volumn 46, Issue 2, 2006, Pages 686-698

  Mpamhanga, Chidochangu P ^a   Chen, Beining ^a   McLay, Iain M ^b   Willett, Peter ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONS; KNOWLEDGE BASED SYSTEMS; KNOWLEDGE ENGINEERING; MOLECULAR WEIGHT; PRINCIPAL COMPONENT ANALYSIS; THREE DIMENSIONAL;

3D BINDING MODES; BISSANTZ ESTROGEN RECEPTOR; KNOWLEDGE-BASED INTERACTION FINGERPRINT SCORING; SCORING FUNCTIONS;

PATTERN RECOGNITION;

ESTROGEN RECEPTOR ALPHA; LIGAND; RALOXIFENE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER SIMULATION; DATA BASE; DRUG ANTAGONISM; DRUG DESIGN; PROTEIN BINDING;

CLUSTER ANALYSIS; COMPUTER SIMULATION; DATABASES; DRUG DESIGN; ESTROGEN RECEPTOR ALPHA; LIGANDS; MOLECULAR STRUCTURE; PROTEIN BINDING; RALOXIFENE;

EID: 33646253652     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050420d     Document Type: Conference Paper

References (35)

1. Deng, Z.; Chuaqui, C.; Singh, J. Structural Interaction Fingerprint (SiFT): A Novel Method for Analysing Three-Dimensional Protein-Ligand Binding Interactions. J. Med. Chem. 2004, 47, 337-344.
2. 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.
3. Perola, E.; Walters, W. P.; Charifson, P. S. A Detailed Comparison of Current Docking and Scoring Methods On Systems Of Pharmaceutical Relevance. Proteins 2004, 56, 235-249.
4. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. A Review of Protein-Small Molecule Docking Methods. J. Comput.-Aided, Mol. Des. 2002, 16, 151-166.
5. Bohm, H.; Stahl, M. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Indiana University-Purdue University and Wiley-VCH: Hoboken, NJ, 2002; Vol. 18, Chapter 2, pp 41-87.
6. Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus Scoring: A Method For Obtaining Improved Hit Rates From Docking Databases Of Three-Dimensional Structures Into Proteins. J. Med. Chem. 1999, 42, 5100-5109.
7. Mpamhanga, C. P.; Chen, B.; Mclay, I. M.; Ormsby, D.; Lindvall M. K. A Retrospective Docking Study Of PDE4B Ligands And An Analysis Of The Behaviour Of Selected Scoring Functions. J. Chem. Inf. Model. 2005, 45, 1061-1074.
8. Feher, M.; Deretey, E.; Roy, S. BHB: A Simple Knowledge-Based Scoring Function to Improve the Efficiency of Database Screening. J. Chem. Inf. Comput. Sci. 2003, 43, 1316-1327.
9. Verdonk, M. L. B.; Hartshorn, M. J.; Mooij, W. T. M.; Murray, C. W.; Taylor, R. D.; Watson, P. Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment. J. Chem. Inf. Comput Sci. 2004, 44, 793-806.
10. Fradera, X.; Knegtel, R. M. A.; Mestres, J. Similarity-Driven Flexible Ligand Docking. Proteins: Struct., Funct., Genet. 2000, 40, 623-636.
11. Bernacki, K.; Kalyanaraman, C.; Jacobson, M. P. Virtual Ligand Screening against Escherichia coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods. J. Biomol. Screening [Online] 2005, 10, 675-681.
12. Carhart, R. S.; Smith, D. H.; Venkataraghava, R. Atom Pairs as Molecular Features in Structure - Activity Studies: Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
13. Willett, P. W.; Bawden, D. Implementation of Nearest Neighbour Searching in an Online Chemical Structure Search System. J. Chem. Inf. Comput. Sci. 1986, 26, 36-41.
14. Fisanick, W. C.; Rusinko, A. Similarity Searching on CAS Registry Substances. 1. Global Molecular Property and Generic Atom Triangle Geometric Searching. J. Chem. Inf. Comput. Sci. 1992, 32, 664-674.
15. Hagadone, T. R. Molecular Substructure Similarity Searching: Efficient Retrieval in Two-Dimensional Structure Databases. J. Chem. Inf. Comput. Sci. 1992, 32, 515-521.
16. Downs, G. M. W.; Fisanick, W. Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. J. Chem. Inf. Comput. Sci. 1994, 34, 1094-1102.
17. Brown, R. D. M. 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.
18. Kearsley, S. K. S.; Fluder, E. M.; Andose, J. D.; Mosley, R. T.; Sheriden, R. P. Chemical Similarity Using Physiochemical Property Descriptors. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127.
19. Thorner, D. A. W.; Willett, P.; Wright, P. M. Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials. J. Chem. Inf. Comput. Sci. 1996, 36, 900-908.
20. Lewis, R. A.; Mason, J. S.; McLay, I. M. Similarity Measures for Rational Set Selection and Analysis of Combinatorial Libraries: The Diverse Property-Derived (DPD) Approach. J. Chem. Inf. Comput. Sci. 1997, 37, 559-614.
21. Willett, P. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
22. 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.
23. Daylight. http://www.daylight.com (accessed Sept 2005).
24. Taylor, R.; Mullier, G. W.; Sexton, G. J. Automation of Conformational Analysis and other Molecular Modeling Calculations. J. Mol. Graphics 1992, 10, 152-160.
25. Tripos. http://www.tripos.com (accessed Sept 2005).
26. Jones, G. W.; 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.
27. Shiau, A. K.; Barstad, D.; Loria, P. M.; Cheng, L.; Kushner, P. J.; Agard, D. A.; Greene, G. L. The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of this Interaction by Tamoxifen. Cell 1998, 95, 927-937.
28. Brzozowski, A. M.; Pike, A. C.; Dauter, Z.; Hubbard, R. E.; Bonn, T.; Engstrom, O.; Ohman, L.; Greene, G. L.; Gustafsson, J. A.; Carlquist, M. Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor. Nature 1997, 389, 753-758.
29. Rognan dataset. www.bioinfo-pharma.u-strasbg.fr/download/random1000.mol/ (accessed Sept 2005).
30. 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.
31. Smith, L. I. A Tutorial on Principal Component Analysis. www.cs.otago.ac.nz/student_tutorials/ (accessed Sept 2005).
32. Spotfire. http://www.spotfire.com (accessed Sept 2005).
33. Kelly, M. D.; Mancera, R. L. Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design. J. Chem. Inf. Comput. Sci. 2004, 44, 1942-1951.
34. Ewing, T., Kuntz, I. D. Critical Evaluation of Search Algorithms for Automated Molecular Docking and Database Screening. J. Comput. Chem. 1997, 18, 1175-189.
35. Mason, J. S.; Beno, B. R. Library Design Using BCUT Chemistry-Space Descriptors and Multiple Four-Point Pharmacophore Fingerprints: Simultaneous Optimization and Structure-Based Diversity. J. Mol. Graphics Modell. 2000, 18, 438-451.