메뉴 건너뛰기




Volumn 46, Issue 2, 2006, Pages 587-596

A knowledge-based weighting approach to ligand-based virtual screening

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; COMPUTER SYSTEMS PROGRAMMING; DATA REDUCTION; DRUG PRODUCTS; GRAPH THEORY; KNOWLEDGE BASED SYSTEMS; MOLECULAR STRUCTURE; MUTAGENESIS; NUCLEAR MAGNETIC RESONANCE; PROTEINS; SCAFFOLDS; SET THEORY; SURFACE PLASMON RESONANCE; VIRTUAL REALITY; X RAYS;

EID: 33646261627     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050324c     Document Type: Conference Paper
Times cited : (27)

References (38)
  • 1
    • 0016381211 scopus 로고
    • A novel approach to the problem of drug design
    • Cramer, R. D., III.; Redl, G.; Berkoff, C. E. A Novel Approach to the Problem of Drug Design. J. Med. Chem. 1974, 17, 533-535.
    • (1974) J. Med. Chem. , vol.17 , pp. 533-535
    • Cramer III, R.D.1    Redl, G.2    Berkoff, C.E.3
  • 2
    • 0036214750 scopus 로고    scopus 로고
    • Virtual screening in drug discovery: Methods, expectations and reality
    • Bajorath, J. Virtual Screening in Drug Discovery: Methods, Expectations and Reality. Curr. Drug Discovery 2002, 3, 25-28.
    • (2002) Curr. Drug Discovery , vol.3 , pp. 25-28
    • Bajorath, J.1
  • 3
    • 0036740917 scopus 로고    scopus 로고
    • Why do we need so many chemical similarity search methods?
    • Sheridan, R. P.; Kearsley, S. K. Why do we need so many Chemical Similarity Search Methods? Drug Discover? Today 2002, 7, 903-911.
    • (2002) Drug Discover? Today , vol.7 , pp. 903-911
    • Sheridan, R.P.1    Kearsley, S.K.2
  • 4
    • 0036007208 scopus 로고    scopus 로고
    • Virtual screening and fast automated docking methods
    • Schneider, G.; Böhm, H.-J. Virtual Screening and Fast Automated Docking Methods. Drug Discovery Today 2002, 7, 64-70.
    • (2002) Drug Discovery Today , vol.7 , pp. 64-70
    • Schneider, G.1    Böhm, H.-J.2
  • 5
    • 10344230435 scopus 로고    scopus 로고
    • Molecular similarity: A key technique in molecular informatics
    • Bender, A.; Glen, R. C. Molecular Similarity: a Key Technique in Molecular Informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
    • (2004) Org. Biomol. Chem. , vol.2 , pp. 3204-3218
    • Bender, A.1    Glen, R.C.2
  • 7
    • 0037361941 scopus 로고    scopus 로고
    • Combination of fingerprint-based similarity coefficients using data fusion
    • Salim, N.; Holliday, J.; Willett, P. Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion. J. Chem. Inf. Comput. Sci. 2003, 43, 435-442.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 435-442
    • Salim, N.1    Holliday, J.2    Willett, P.3
  • 8
    • 0035438388 scopus 로고    scopus 로고
    • Prediction of biological activity for high-throughput screening using binary kernel discrimination
    • Harper, G.; Bradshaw, J.; Gittins, J. C.; Green, D. V. S.; Leach, A. R. Prediction of Biological Activity for High-Throughput Screening Using Binary Kernel Discrimination. J. Chem. Inf. Comput. Sci. 2001, 41, 1295-1300.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1295-1300
    • Harper, G.1    Bradshaw, J.2    Gittins, J.C.3    Green, D.V.S.4    Leach, A.R.5
  • 9
    • 1842690601 scopus 로고    scopus 로고
    • Molecular similarity searching using atom environments, information-based feature selection, and a naïve bayesian classifier
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 170-178
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3    Reiling, S.4
  • 10
    • 5544290537 scopus 로고    scopus 로고
    • Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 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
  • 11
    • 10844249112 scopus 로고    scopus 로고
    • Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D)
    • Bender, A.; Mussa, H. Y.; Gill, G. S.; Glen, R. C. Molecular Surface Point Environments for Virtual Screening and the Elucidation of Binding Patterns (MOLPRINT 3D). J. Med. Chem. 2004, 47. 6569-6583.
    • (2004) J. Med. Chem. , vol.47 , pp. 6569-6583
    • Bender, A.1    Mussa, H.Y.2    Gill, G.S.3    Glen, R.C.4
  • 12
    • 0043201432 scopus 로고    scopus 로고
    • Profile scaling increases the similarity search performance of molecular fingerprints containing numerical descriptors and structural keys
    • Xue, L.; Godden, J. W.; Stahura, F. L.; Bajorath, J. Profile Scaling Increases the Similarity Search Performance of Molecular Fingerprints Containing Numerical Descriptors and Structural Keys. J. Chem. Inf. Comput. Sci. 2003, 43, 1218-1225.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 1218-1225
    • Xue, L.1    Godden, J.W.2    Stahura, F.L.3    Bajorath, J.4
  • 13
    • 10044240762 scopus 로고    scopus 로고
    • Similarity search profiling reveals effects of fingerprint scaling in virtual screening
    • Xue, L.; Stahura, F. L.; Bajorath, J. Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening. J. Chem. Inf. Comput. Sci. 2004, 44, 2032-2039.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 2032-2039
    • Xue, L.1    Stahura, F.L.2    Bajorath, J.3
  • 14
    • 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
  • 16
    • 0346962971 scopus 로고    scopus 로고
    • Structural Interaction Fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions
    • Deng, Z.; Chuaqui, C.; Singh, J. Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions. J. Med. Chem. 2004, 47, 337-344.
    • (2004) J. Med. Chem. , vol.47 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 17
    • 12144249613 scopus 로고    scopus 로고
    • Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening
    • Chuaqui, C.; Deng, Z.; Singh, J. Interaction Profiles of Protein Kinase-Inhibitor Complexes and Their Application to Virtual Screening. J. Med. Chem. 2005, 48. 121-133.
    • (2005) J. Med. Chem. , vol.48 , pp. 121-133
    • Chuaqui, C.1    Deng, Z.2    Singh, J.3
  • 22
    • 33646271978 scopus 로고    scopus 로고
    • DAYLIGHT Inc., Mission Viejo, CA
    • DAYLIGHT Inc., Mission Viejo, CA.
  • 23
    • 21744438303 scopus 로고    scopus 로고
    • Tripos Inc.: St. Louis, Missouri
    • SYBYL, version 7.0: Tripos Inc.: St. Louis, Missouri, 2004.
    • (2004) SYBYL, Version 7.0
  • 24
    • 0032149905 scopus 로고    scopus 로고
    • Feature trees: A new molecular similarity measure based on tree matching
    • Rarey, M.; Dixon, J. S. Feature Trees: A New Molecular Similarity Measure Based on Tree Matching. J. Comput.-Aided Mol. Des. 1998, 12, 471-490.
    • (1998) J. Comput.-aided Mol. Des. , vol.12 , pp. 471-490
    • Rarey, M.1    Dixon, J.S.2
  • 25
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 26
    • 0036025430 scopus 로고    scopus 로고
    • An alignment-independent versatile structure descriptor for QSAR and QSPR based on the distribution of molecular features
    • Baumann, K. An Alignment-Independent Versatile Structure Descriptor for QSAR and QSPR Based on the Distribution of Molecular Features. J. Chem. Inf. Comput. Sci. 2002, 42, 26-35.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 26-35
    • Baumann, K.1
  • 27
    • 0037431388 scopus 로고    scopus 로고
    • Mapping property distributions of molecular surfaces: Algorithm and evaluation of a novel 3D quantitative structure-activity relationship technique
    • Stiefl, N.; Baumann, K. Mapping Property Distributions of Molecular Surfaces: Algorithm and Evaluation of a Novel 3D Quantitative Structure-Activity Relationship Technique. J. Med. Chem. 2003, 46. 1390-1407.
    • (2003) J. Med. Chem. , vol.46 , pp. 1390-1407
    • Stiefl, N.1    Baumann, K.2
  • 29
    • 0036827080 scopus 로고    scopus 로고
    • Performance of similarity measures in 2D fragment-based similarity searching: Comparison of structural descriptors and similarity coefficients
    • Chen, X.; Reynolds, C. H. Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2002, 42, 1407-1414.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 1407-1414
    • Chen, X.1    Reynolds, C.H.2
  • 30
    • 0032226476 scopus 로고    scopus 로고
    • Development of filter functions for protein-ligand docking
    • Stahl, M.; Böhm, H.-J. Development of Filter Functions for Protein-Ligand Docking. J. Mol. Graphics Modell. 1998, 16, 121-132.
    • (1998) J. Mol. Graphics Modell. , vol.16 , pp. 121-132
    • Stahl, M.1    Böhm, H.-J.2
  • 31
    • 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
  • 33
    • 33646236586 scopus 로고    scopus 로고
    • Molecular Networks: Erlangen, Germany
    • CORINA; Molecular Networks: Erlangen, Germany.
    • CORINA
  • 34
    • 2942699446 scopus 로고    scopus 로고
    • MDL Information Systems Inc., San Leandro, CA
    • The MDL Drug Data Report database is available from MDL Information Systems Inc., San Leandro, CA.
    • The MDL Drug Data Report Database
  • 35
    • 33646269298 scopus 로고    scopus 로고
    • (accessed May 2005)
    • Brookhaven Protein Databank. http://www.rcsb.org (accessed May 2005).
  • 36
    • 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. Comput. Sci. 2001, 41, 1395-1406.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1395-1406
    • Sheridan, R.P.1    Singh, S.B.2    Fluder, E.M.3    Kearsley, S.K.4
  • 37
    • 33646740651 scopus 로고    scopus 로고
    • Parameter estimation for scoring protein-ligand interactions using negative training data
    • [ASAP article], DOI: 10.1021/jm050040j
    • Pham, T. A.; Jain, A. N. Parameter Estimation for Scoring Protein-Ligand Interactions Using Negative Training Data. J. Med. Chem. [ASAP article] 2005, DOI: 10.1021/jm050040j.
    • (2005) J. Med. Chem.
    • Pham, T.A.1    Jain, A.N.2
  • 38
    • 0035843962 scopus 로고    scopus 로고
    • Structural mechanism for statin inhibition of HMG-CoA reductase
    • Istvan, E. S.; Deisenhofer, J. Structural Mechanism for Statin Inhibition of HMG-CoA Reductase. Science 2001, 292, 1160-1164.
    • (2001) Science , vol.292 , pp. 1160-1164
    • Istvan, E.S.1    Deisenhofer, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.