메뉴 건너뛰기




Volumn 46, Issue 2, 2006, Pages 844-851

Chemometric analysis of ligand receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTATIONAL GEOMETRY; DATABASE SYSTEMS; MOLECULAR STRUCTURE; VECTORS; X RAY ANALYSIS;

EID: 33646251585     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050065r     Document Type: Conference Paper
Times cited : (53)

References (40)
  • 1
    • 0027385177 scopus 로고
    • Matching chemistry and shape in molecular docking
    • Shoichet, B. K.; Kuntz, I. D. Matching Chemistry and Shape in Molecular Docking. Protein Eng. 1993, 6, 723-732.
    • (1993) Protein Eng. , vol.6 , pp. 723-732
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 5
    • 0029705324 scopus 로고    scopus 로고
    • Automated docking of flexible ligands: Applications of AutoDock
    • Goodsell, D. S.; Morris, G. M.; Olson, A. J. Automated docking of flexible ligands: Applications of AutoDock. J. Mol. Recognit. 1996, 9, 1-5.
    • (1996) J. Mol. Recognit. , vol.9 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 6
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002, 46, 34-40.
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 7
    • 0035765452 scopus 로고    scopus 로고
    • Small molecule docking and scoring
    • Lipkowitz, K. B., Boyd, D. B., Eds.; John Wiley & Sons
    • Muegge, I.; Rarey, M. Small Molecule Docking and Scoring. In Reviews in Computational Chemistry, 17th ed.; Lipkowitz, K. B., Boyd, D. B., Eds.; John Wiley & Sons: 2001.
    • (2001) Reviews in Computational Chemistry, 17th Ed.
    • Muegge, I.1    Rarey, M.2
  • 8
    • 8744243346 scopus 로고
    • Molecular-dynamics and free-energy perturbation calculations - What role do they play in computer-assisted molecular design
    • Kollman, P. Molecular-Dynamics and Free-Energy Perturbation Calculations - What Role Do They Play in Computer-Assisted Molecular Design. FASEB J. 1995, 9, A1253-A1253.
    • (1995) FASEB J. , vol.9
    • Kollman, P.1
  • 9
    • 7044239742 scopus 로고
    • Free-energy calculations - Applications to chemical and biochemical phenomena
    • Kollman, P. Free-Energy Calculations - Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 10
    • 0036280661 scopus 로고    scopus 로고
    • Ligand binding affinities from MD simulations
    • Aqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Ligand binding affinities from MD simulations. Acc. Chem. Res. 2002, 35, 358-365.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 358-365
    • Aqvist, J.1    Luzhkov, V.B.2    Brandsdal, B.O.3
  • 11
    • 0028155689 scopus 로고
    • New method for predicting binding-affinity in computer-aided drug design
    • Aqvist, J.; Medina, C.; Samuelsson, J. E. New Method for Predicting Binding-Affinity in Computer-Aided Drug Design. Protein Eng. 1994, 7, 385-391.
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 12
    • 0346052295 scopus 로고    scopus 로고
    • Calculation of the hydration free energies using an extended linear response method
    • Chen, X.; Tropsha, A. Calculation of the hydration free energies using an extended linear response method. J. Comput. Chem. 1999, 20, 749-759.
    • (1999) J. Comput. Chem. , vol.20 , pp. 749-759
    • Chen, X.1    Tropsha, A.2
  • 13
    • 0035950792 scopus 로고    scopus 로고
    • New linear interaction method for binding affinity calculations using a continuum solvent model
    • Zhou, R. H.; Friesner, R. A.; Ghosh, A.; Rizzo, R. C.; Jorgensen, W. L.; Levy, R. M. New linear interaction method for binding affinity calculations using a continuum solvent model. J. Phys. Chem. B 2001, 105, 10388-10397.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 10388-10397
    • Zhou, R.H.1    Friesner, R.A.2    Ghosh, A.3    Rizzo, R.C.4    Jorgensen, W.L.5    Levy, R.M.6
  • 14
    • 20444411998 scopus 로고    scopus 로고
    • Recent trends in quantitative structure-activity relationships
    • Abraham, D., Ed.; John Wiley & Sons: New York
    • Tropsha, A. Recent Trends in Quantitative Structure-Activity Relationships. In Burger's Medicinal Chemistry and Drug Discovery, 6th ed.; Abraham, D., Ed.; John Wiley & Sons: New York, 2003; pp 49-77.
    • (2003) Burger's Medicinal Chemistry and Drug Discovery, 6th Ed. , pp. 49-77
    • Tropsha, A.1
  • 15
    • 0000353230 scopus 로고    scopus 로고
    • The characterization of chemical structures using molecular properties
    • Livingstone, D. J. The characterization of chemical structures using molecular properties. J. Chem. Inf. Comput. Sci 2000, 40, 195-209.
    • (2000) J. Chem. Inf. Comput. Sci , vol.40 , pp. 195-209
    • Livingstone, D.J.1
  • 16
    • 0033968062 scopus 로고    scopus 로고
    • Chemoinformatics - Similarity and diversity in chemical libraries
    • Willett, P. Chemoinformatics - similarity and diversity in chemical libraries. Curr. Opin. Biotechnol. 2000, 11, 85-88.
    • (2000) Curr. Opin. Biotechnol. , vol.11 , pp. 85-88
    • Willett, P.1
  • 17
    • 0033980580 scopus 로고    scopus 로고
    • Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA)
    • Turner, D. B.; Willett, P. Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA). J. Comput.-Aided Mol. Des. 2000, 14, 1-21.
    • (2000) J. Comput.-aided Mol. Des. , vol.14 , pp. 1-21
    • Turner, D.B.1    Willett, P.2
  • 18
    • 0000886672 scopus 로고
    • Electron density modeling of large systems using the transferable atom equivalent method
    • Breneman, C. M.; Thompson, T. R.; Rhem, M; Dung, M. Electron Density Modeling of Large Systems using the Transferable Atom Equivalent Method. Comput. Chem. 1995, 19, 161-169.
    • (1995) Comput. Chem. , vol.19 , pp. 161-169
    • Breneman, C.M.1    Thompson, T.R.2    Rhem, M.3    Dung, M.4
  • 19
    • 0035891173 scopus 로고    scopus 로고
    • Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure
    • Mazza, C. B.; Sukumar, N.; Breneman, C. M.; Cramer, S. M. Prediction of protein retention in ion-exchange systems using molecular descriptors obtained from crystal structure. Anal. Chem. 2001, 73, 5457-5461.
    • (2001) Anal. Chem. , vol.73 , pp. 5457-5461
    • Mazza, C.B.1    Sukumar, N.2    Breneman, C.M.3    Cramer, S.M.4
  • 20
    • 0036827078 scopus 로고    scopus 로고
    • Prediction of protein retention times in anion-exchange chromatography systems using support vector regression
    • Song, M.; Breneman, C. M.; Bi, J.; Sukumar, N.; Bennett. K. P.; Cramer, S.; Tugcu, N. Prediction of protein retention times in anion-exchange chromatography systems using support vector regression. J. Chem. Inf. Comput. Sci. 2002, 42, 1347-1357.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 1347-1357
    • Song, M.1    Breneman, C.M.2    Bi, J.3    Sukumar, N.4    Bennett, K.P.5    Cramer, S.6    Tugcu, N.7
  • 21
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 2004, 47, 2977-2980.
    • (2004) J. Med. Chem. , vol.47 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 22
    • 28544445099 scopus 로고    scopus 로고
    • Tripos, Inc., St. Louis, MO
    • Tripos Inc. Sybyl User's Manual Version 7.8; Tripos, Inc., St. Louis, MO, 2002.
    • (2002) Sybyl User's Manual Version 7.8
  • 23
    • 0017033395 scopus 로고
    • Molecular connectivity VII: Specific treatment of heteroatoms
    • Kier, L. B.; Hall, L. H. Molecular connectivity VII: specific treatment of heteroatoms. J. Pharm. Sci. 1976, 65, 1806-1809.
    • (1976) J. Pharm. Sci. , vol.65 , pp. 1806-1809
    • Kier, L.B.1    Hall, L.H.2
  • 24
    • 0017133376 scopus 로고
    • Molecular connectivity V: Connectivity series concept applied to density
    • Kier, L. B.; Murray, W. J.; Randic, M.: Hall, L. H. Molecular connectivity V: connectivity series concept applied to density. J. Pharm. Sci. 1976, 65, 1226-1230.
    • (1976) J. Pharm. Sci. , vol.65 , pp. 1226-1230
    • Kier, L.B.1    Murray, W.J.2    Randic, M.3    Hall, L.H.4
  • 25
    • 0016771481 scopus 로고
    • Molecular connectivity. 4. Relationships to biological activities
    • Kier, L. B.; Murray, W. J.; Hall, L. H. Molecular connectivity. 4. Relationships to biological activities. J. Med. Chem. 1975, 18, 1272-1274.
    • (1975) J. Med. Chem. , vol.18 , pp. 1272-1274
    • Kier, L.B.1    Murray, W.J.2    Hall, L.H.3
  • 26
    • 0016771380 scopus 로고
    • Molecular connectivity. I: Relationship to nonspecific local anesthesia
    • Kier, L. B.; Hall, L. H.; Murray, W. J.; Randic, M. Molecular connectivity. I: Relationship to nonspecific local anesthesia. J. Pharm. Sci. 1975, 64, 1971-1974.
    • (1975) J. Pharm. Sci. , vol.64 , pp. 1971-1974
    • Kier, L.B.1    Hall, L.H.2    Murray, W.J.3    Randic, M.4
  • 28
    • 0017100656 scopus 로고
    • Molecular connectivity. 6. Examination of the parabolic relationship between molecular connectivity and biological activity
    • Murray, W. J.; Kier, L. B.; Hall, L. H. Molecular connectivity. 6. Examination of the parabolic relationship between molecular connectivity and biological activity. J. Med. Chem. 1976, 19, 573-578.
    • (1976) J. Med. Chem. , vol.19 , pp. 573-578
    • Murray, W.J.1    Kier, L.B.2    Hall, L.H.3
  • 29
    • 0016830070 scopus 로고
    • Molecular connectivity. III: Relationship to partition coefficients
    • Murray, W. J.; Hall, L. H.; Kier, L. B. Molecular connectivity. III: Relationship to partition coefficients. J. Pharm. Sci. 1975, 64, 1978-1981.
    • (1975) J. Pharm. Sci. , vol.64 , pp. 1978-1981
    • Murray, W.J.1    Hall, L.H.2    Kier, L.B.3
  • 30
    • 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
  • 31
    • 11144354205 scopus 로고    scopus 로고
    • Application of predictive QSAR models to database mining: Identification and experimental validation of novel anticonvulsant compounds
    • Shen, M.; Beguin, C.; Golbraikh, A.; Stables, J. P.; Kohn, H.; Tropsha, A. Application of predictive QSAR models to database mining: identification and experimental validation of novel anticonvulsant compounds. J. Med. Chem. 2004, 47, 2356-2364.
    • (2004) J. Med. Chem. , vol.47 , pp. 2356-2364
    • Shen, M.1    Beguin, C.2    Golbraikh, A.3    Stables, J.P.4    Kohn, H.5    Tropsha, A.6
  • 35
    • 0000378338 scopus 로고    scopus 로고
    • Novel variable selection quantitative structure-property relationship approach based on the k-nearest-neighbor principle
    • Zheng, W.; Tropsha. A. Novel variable selection quantitative structure-property relationship approach based on the k-nearest-neighbor principle. J. Chem. Inf. Comput. Sci. 2000, 40, 185-194.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 185-194
    • Zheng, W.1    Tropsha, A.2
  • 36
    • 0042355453 scopus 로고    scopus 로고
    • Rational selection of training and test sets for the development of validated QSAR models
    • Golbraikh, A.; Shen, M.; Xiao, Z.; Xiao, Y. D.; Lee, K. H.; Tropsha, A. Rational selection of training and test sets for the development of validated QSAR models. J. Comput.-Aided Mol. Des. 2003, 17, 241-253.
    • (2003) J. Comput.-aided Mol. Des. , vol.17 , pp. 241-253
    • Golbraikh, A.1    Shen, M.2    Xiao, Z.3    Xiao, Y.D.4    Lee, K.H.5    Tropsha, A.6
  • 37
    • 0036933967 scopus 로고    scopus 로고
    • Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection
    • Golbraikh, A.; Tropsha, A. Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. Mol. Divers. 2002, 5, 231-243.
    • (2002) Mol. Divers. , vol.5 , pp. 231-243
    • Golbraikh, A.1    Tropsha, A.2
  • 39
    • 0038724207 scopus 로고    scopus 로고
    • The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models
    • Tropsha, A.; Gramatica, P.; Gombar, V. K. The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models. Quant. Struct. Act. Relat. Comb. Sci. 2003, 22, 69-77.
    • (2003) Quant. Struct. Act. Relat. Comb. Sci. , vol.22 , pp. 69-77
    • Tropsha, A.1    Gramatica, P.2    Gombar, V.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.