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Volumn 48, Issue 2, 2008, Pages 319-332

Maximum common binding modes (MCBM): Consensus docking scoring using multiple ligand information and interaction fingerprints

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; LIGANDS; SELF ORGANIZING MAPS;

EID: 41549114720     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci7003626     Document Type: Article
Times cited : (41)

References (77)
  • 1
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of proteinligand interactions. Docking and scoring: Successes and gaps
    • Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. Prediction of proteinligand interactions. Docking and scoring: successes and gaps. J. Med. Chem. 2006, 49, 5851-5855.
    • (2006) J. Med. Chem , vol.49 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 2
    • 33749260698 scopus 로고    scopus 로고
    • A critical assessment of docking programs and scoring functions
    • Warren, G. L., et al. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2006, 49, 5912-5931.
    • (2006) J. Med. Chem , vol.49 , pp. 5912-5931
    • Warren, G.L.1
  • 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 Discovery 2004, 3, 935-949.
    • (2004) Nat. Rev. Drug Discovery , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 4
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem., Int. Ed. Engl. 2002, 41, 2644-2676.
    • (2002) Angew. Chem., Int. Ed. Engl , vol.41 , pp. 2644-2676
    • Gohlke, H.1    Klebe, G.2
  • 5
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • 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.
    • (1999) J. Med. Chem , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 6
    • 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
  • 7
    • 0035438402 scopus 로고    scopus 로고
    • How does consensus scoring work for virtual library screening? An idealized computer experiment
    • Wang, R.; Wang, S. How does consensus scoring work for virtual library screening? An idealized computer experiment. J. Chem. Inf. Comput. Sci. 2001, 41, 1422-1426.
    • (2001) J. Chem. Inf. Comput. Sci , vol.41 , pp. 1422-1426
    • Wang, R.1    Wang, S.2
  • 8
    • 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. S.; Hsu, D. F. 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.S.4    Hsu, D.F.5
  • 9
    • 33344465112 scopus 로고    scopus 로고
    • The use of consensus scoring in ligand-based virtual screening
    • Baber, J. C.; Shirley, W. A.; Gao, Y.; Feher, M. The use of consensus scoring in ligand-based virtual screening. J. Chem. Inf. Model. 2006, 46, 277-288.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 277-288
    • Baber, J.C.1    Shirley, W.A.2    Gao, Y.3    Feher, M.4
  • 10
    • 33644862638 scopus 로고    scopus 로고
    • Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring
    • Zhang, Q.; Muegge, I. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring. J. Med. Chem. 2006, 49, 1536-1548.
    • (2006) J. Med. Chem , vol.49 , pp. 1536-1548
    • Zhang, Q.1    Muegge, I.2
  • 11
    • 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, 435-342.
    • (2003) J Chem. Inf. Comput. Sci , vol.43 , pp. 435-342
    • Salim, N.1    Holliday, J.2    Willett, P.3
  • 12
    • 3242729478 scopus 로고    scopus 로고
    • Evaluation of distance metrics for ligand-based similarity searching
    • Fechner, U.; Schneider, G. Evaluation of distance metrics for ligand-based similarity searching. ChemBioChem 2004, 5, 538-540.
    • (2004) ChemBioChem , vol.5 , pp. 538-540
    • Fechner, U.1    Schneider, G.2
  • 13
    • 0029970338 scopus 로고    scopus 로고
    • Evolutionary optimization in quantitative structure-activity relationship: An application of genetic neural networks
    • So, S.-S.; Karplus, M. Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural networks. J. Med. Chem. 1996, 39, 1521-1530.
    • (1996) J. Med. Chem , vol.39 , pp. 1521-1530
    • So, S.-S.1    Karplus, M.2
  • 14
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman, L. Random Forests. Machine Learning 2001, 45, 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 17
    • 5444268169 scopus 로고    scopus 로고
    • Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: A comparison of similarity coefficients
    • Whittle, M.; Gillet, V. J.; Willett, P.; Alex, A.; Loesel, J. Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficients. J. Chem. Inf. Comput. Sci. 2004, 44, 1840-1848.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 1840-1848
    • Whittle, M.1    Gillet, V.J.2    Willett, P.3    Alex, A.4    Loesel, J.5
  • 18
    • 1842690601 scopus 로고    scopus 로고
    • Molecular similarity searching using atom environments, information-based feature selection, and a naive Bayesian classifier
    • Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular similarity searching using atom environments, information-based feature selection, and a naive 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
  • 19
    • 27444433232 scopus 로고    scopus 로고
    • Extraction and visualization of potential pharmacophore points using support vector machines: Application to ligand-based virtual screening for COX-2 inhibitors
    • Franke, L.; Byvatov, E.; Werz, O.; Steinhilber, D.; Schneider, P.; Schneider, G. Extraction and visualization of potential pharmacophore points using support vector machines: application to ligand-based virtual screening for COX-2 inhibitors. J. Med. Chem. 2005, 48, 6997-7004.
    • (2005) J. Med. Chem , vol.48 , pp. 6997-7004
    • Franke, L.1    Byvatov, E.2    Werz, O.3    Steinhilber, D.4    Schneider, P.5    Schneider, G.6
  • 20
    • 33646249968 scopus 로고    scopus 로고
    • New methods for ligand-based virtual screening: Use of data fusion and machine learning to enhance the effectiveness of similarity searching
    • Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching. J. Chem. Inf. Model. 2006, 46, 462-470.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 462-470
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 22
    • 84952890016 scopus 로고    scopus 로고
    • Langer, T, Hoffmann, R. D, Eds, Wiley-VCH: Weinheim
    • Pharmacophores and Pharmacophore Searches; Langer, T., Hoffmann, R. D., Eds.; Wiley-VCH: Weinheim, 2006.
    • (2006) Pharmacophores and Pharmacophore Searches
  • 23
    • 4444275159 scopus 로고    scopus 로고
    • Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening
    • Renner, S.; Schneider, G. Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening. J. Med. Chem. 2004, 47, 4653-4664.
    • (2004) J. Med. Chem , vol.47 , pp. 4653-4664
    • Renner, S.1    Schneider, G.2
  • 24
    • 33750981540 scopus 로고    scopus 로고
    • Do structurally similar ligands bind in a similar fashion
    • Boström, J.; Hogner, A.; Schmitt, S. Do structurally similar ligands bind in a similar fashion. J. Med. Chem. 2006, 49, 6716-6725.
    • (2006) J. Med. Chem , vol.49 , pp. 6716-6725
    • Boström, J.1    Hogner, A.2    Schmitt, S.3
  • 25
    • 23244436580 scopus 로고    scopus 로고
    • Optimal clustering for detecting near-native conformations in protein docking
    • Kozakov, A.; Clodfelter, K. H.; Vajda, S.; Camacho, C. J. Optimal clustering for detecting near-native conformations in protein docking. Biophys. J. 2005, 89, 867-875.
    • (2005) Biophys. J , vol.89 , pp. 867-875
    • Kozakov, A.1    Clodfelter, K.H.2    Vajda, S.3    Camacho, C.J.4
  • 27
    • 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
  • 28
    • 10044263239 scopus 로고    scopus 로고
    • Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design
    • 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.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 1942-1951
    • Kelly, M.D.1    Mancera, R.L.2
  • 29
    • 33244464010 scopus 로고    scopus 로고
    • VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening
    • Amari, S.; Aizawa, M.; Zhang, J.; Fukuzawa, K.; Mochizuki, Y.; Iwasawa, Y.; Nakata, K.; Chuman, H.; Nakano, T. VISCANA: visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening. J. Chem. Inf. Model. 2006, 46, 221-230.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 221-230
    • Amari, S.1    Aizawa, M.2    Zhang, J.3    Fukuzawa, K.4    Mochizuki, Y.5    Iwasawa, Y.6    Nakata, K.7    Chuman, H.8    Nakano, T.9
  • 30
    • 33646253652 scopus 로고    scopus 로고
    • Knowledge-based interaction fingerprint scoring: A simple method for improving the effectiveness of fast scoring functions
    • Mpamhanga, C. P.; Chen, B.; McLay, I. M.; Willett, P. Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions. J. Chem. Inf. Model. 2006, 46, 686-698.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 686-698
    • Mpamhanga, C.P.1    Chen, B.2    McLay, I.M.3    Willett, P.4
  • 31
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
    • Marcou, G.; Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J. Chem. Inf. Model. 2007, 47, 195-207.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 32
    • 12144249613 scopus 로고    scopus 로고
    • Interaction profiles of protein kinaseinhibitor complexes and their application to virtual screening
    • Chuaqui, C.; Deng, Z.; Singh, J. Interaction profiles of protein kinaseinhibitor complexes and their application to virtual screening. J. Med. Chem. 2005, 48, 121-33.
    • (2005) J. Med. Chem , vol.48 , pp. 121-133
    • Chuaqui, C.1    Deng, Z.2    Singh, J.3
  • 33
    • 0034284367 scopus 로고    scopus 로고
    • Similarity driven flexible ligand docking
    • Fradera, X.; Knetgel, R. M.; Mestres, J. Similarity driven flexible ligand docking. Proteins 2000, 40, 623-636.
    • (2000) Proteins , vol.40 , pp. 623-636
    • Fradera, X.1    Knetgel, R.M.2    Mestres, J.3
  • 34
    • 2542543615 scopus 로고    scopus 로고
    • SDOCKER: A method utilizing existing X-ray structures to improve docking accuracy
    • Wu, G.; Vieth, M. SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy. J. Med. Chem. 2004, 47, 3142-3148.
    • (2004) J. Med. Chem , vol.47 , pp. 3142-3148
    • Wu, G.1    Vieth, M.2
  • 36
    • 23944499528 scopus 로고    scopus 로고
    • Improving binding mode predictions by docking into protein-specifically adapted potential fields
    • Radestock, S.; Bohm, M.; Gohlke, H. Improving binding mode predictions by docking into protein-specifically adapted potential fields. J. Med. Chem. 2005, 48 5466-5479.
    • (2005) J. Med. Chem , vol.48 , pp. 5466-5479
    • Radestock, S.1    Bohm, M.2    Gohlke, H.3
  • 37
    • 0020068152 scopus 로고
    • Self-organized formation of topologically correct feature maps
    • Kohonen, T. Self-organized formation of topologically correct feature maps. Biol. Cybern. 1982, 43, 59-69.
    • (1982) Biol. Cybern , vol.43 , pp. 59-69
    • Kohonen, T.1
  • 38
    • 0030339936 scopus 로고    scopus 로고
    • The comparison of geometric and electronic properties of molecular surfaces by neural networks: Application to the analysis of corticosteroid-binding globulin activity of steroids
    • Anzali, S.; Barnickel, G.; Krug, M.; Sadowski, J.; Wagener, M.; Gasteiger, J.; Polanski, J. The comparison of geometric and electronic properties of molecular surfaces by neural networks: application to the analysis of corticosteroid-binding globulin activity of steroids. J. Comput.-Aided Mol. Des. 1996, 10, 521-534.
    • (1996) J. Comput.-Aided Mol. Des , vol.10 , pp. 521-534
    • Anzali, S.1    Barnickel, G.2    Krug, M.3    Sadowski, J.4    Wagener, M.5    Gasteiger, J.6    Polanski, J.7
  • 39
    • 33750357203 scopus 로고    scopus 로고
    • Predicting compound selectivity by self-organizing maps: Crossactivities of metabotropic glutamate receptor antagonists
    • Noske, T.; Sasse, B. C.; Stark, H.; Parsons, C. G.; Weil, T.; Schneider, G. Predicting compound selectivity by self-organizing maps: crossactivities of metabotropic glutamate receptor antagonists. Chem. Med. Chem. 2006, 1, 1066-1068.
    • (2006) Chem. Med. Chem , vol.1 , pp. 1066-1068
    • Noske, T.1    Sasse, B.C.2    Stark, H.3    Parsons, C.G.4    Weil, T.5    Schneider, G.6
  • 40
    • 0036706746 scopus 로고    scopus 로고
    • A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP
    • Patel, Y.; Gillet, V. J.; Bravi, G.; Leach, A. R. A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. J. Comput.-Aided Mol. Des. 2002, 16, 653-681.
    • (2002) J. Comput.-Aided Mol. Des , vol.16 , pp. 653-681
    • Patel, Y.1    Gillet, V.J.2    Bravi, G.3    Leach, A.R.4
  • 45
    • 2942522534 scopus 로고    scopus 로고
    • Pevarello, P.; Brasca, M. G.; Amici, R.; Orsini, P.; Traquandi, G.; Corti, L.; Piutti, C.; Sansonna, P.; Villa, M.; Pierce, B. S.; Pulici, M.; Giordano, P.; Martina, K.; Fritzen, E. L.; Nugent, R. A.; Casale, E.; Cameron, A.; Ciomei, M.; Roletto, F.; Isacchi, A.; Fogliatto, G.; Pesenti, E.; Pastori, W.; Marsiglio, A.; Leach, K. L.; Clare, P. M.; Fiorentini, F.; Varasi, M.; Vulpetti, A.; Warpehoski, M. A. 3-Aminopyrazole inhibitors of CDK2/cyclin A as antitumor agents. 1. Lead finding. J. Med. Chem. 2004, 47, 3367-3380.
    • Pevarello, P.; Brasca, M. G.; Amici, R.; Orsini, P.; Traquandi, G.; Corti, L.; Piutti, C.; Sansonna, P.; Villa, M.; Pierce, B. S.; Pulici, M.; Giordano, P.; Martina, K.; Fritzen, E. L.; Nugent, R. A.; Casale, E.; Cameron, A.; Ciomei, M.; Roletto, F.; Isacchi, A.; Fogliatto, G.; Pesenti, E.; Pastori, W.; Marsiglio, A.; Leach, K. L.; Clare, P. M.; Fiorentini, F.; Varasi, M.; Vulpetti, A.; Warpehoski, M. A. 3-Aminopyrazole inhibitors of CDK2/cyclin A as antitumor agents. 1. Lead finding. J. Med. Chem. 2004, 47, 3367-3380.
  • 46
    • 15144358589 scopus 로고    scopus 로고
    • Structure-based design and synthesis of lipophilic 2,4-diamino-6substituted quinazolines and their evaluation as inhibitors of dihydrofolate reductases and potential antitumor agents
    • Gangjee, A.; Vidwans, A. P.; Vasudevan, A.; Queener, S. F.; Kisliuk, R. L.; Cody, V.; Li, R.; Galitsky, N.; Luft, J. R.; Pangborn, W. Structure-based design and synthesis of lipophilic 2,4-diamino-6substituted quinazolines and their evaluation as inhibitors of dihydrofolate reductases and potential antitumor agents. J. Med. Chem. 1998, 41, 3426-3434.
    • (1998) J. Med. Chem , vol.41 , pp. 3426-3434
    • Gangjee, A.1    Vidwans, A.P.2    Vasudevan, A.3    Queener, S.F.4    Kisliuk, R.L.5    Cody, V.6    Li, R.7    Galitsky, N.8    Luft, J.R.9    Pangborn, W.10
  • 47
    • 0031798641 scopus 로고    scopus 로고
    • Comparison of ternary crystal complexes of F31 variants of human dihydrofolate reductase with NADPH and a classical antitumor furopyrimidine
    • Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Blakley, R. L.; Gangjee, A. Comparison of ternary crystal complexes of F31 variants of human dihydrofolate reductase with NADPH and a classical antitumor furopyrimidine. Anticancer Drug. Des. 1998, 13, 307-315.
    • (1998) Anticancer Drug. Des , vol.13 , pp. 307-315
    • Cody, V.1    Galitsky, N.2    Luft, J.R.3    Pangborn, W.4    Blakley, R.L.5    Gangjee, A.6
  • 48
    • 0023931977 scopus 로고
    • Crystal structure of human dihydrofolate reductase complexed with folate
    • Oefner, C.; D'Arey, A.; Winkler, F. K. Crystal structure of human dihydrofolate reductase complexed with folate. Eur. J. Biochem. 1988, 174, 377-385.
    • (1988) Eur. J. Biochem , vol.174 , pp. 377-385
    • Oefner, C.1    D'Arey, A.2    Winkler, F.K.3
  • 49
    • 0030656217 scopus 로고    scopus 로고
    • Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523
    • Cody, V.; Galitsky, N.; Luft, J. R.; Pangborn, W.; Rosowsky, A.; Blakley, R. L. Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523. Biochemistry 1997, 36, 13897-13903.
    • (1997) Biochemistry , vol.36 , pp. 13897-13903
    • Cody, V.1    Galitsky, N.2    Luft, J.R.3    Pangborn, W.4    Rosowsky, A.5    Blakley, R.L.6
  • 50
    • 0025037428 scopus 로고
    • Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate
    • Davies, J. F., II; Delcamp, T. J.; Prendergast, N. J.; Ashford, V. A.; Freisheim, J. H.; Kraut, J. Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate. Biochemistry 1990, 29, 9467-9479,
    • (1990) Biochemistry , vol.29 , pp. 9467-9479
    • Davies II, J.F.1    Delcamp, T.J.2    Prendergast, N.J.3    Ashford, V.A.4    Freisheim, J.H.5    Kraut, J.6
  • 56
    • 9544235162 scopus 로고    scopus 로고
    • Lam, P. Y.; Ru, Y.; Jadhav, P. K.; Aldrich, P. E.; DeLucca, G. V.; Eyermann, C. J.; Chang, C. H.; Emmett, G.; Holler, E. R.; Daneker, W. F.; Li, L.; Confalone, P. N.; McHugh, R. J.; Han, Q.; Li, R.; Markwalder, J. A.; Seitz, S. P.; Sharpe, T. R.; Bacheler, L. T.; Rayner, M. M.; Klabe, R. M.; Shum, L.; Winslow, D. L.; Kornhauser, D. M.; Hodge, C. N. et al. Cyclic HIV protease inhibitors: synthesis, conformational analysis, P2/P2′ structure-activity relationship, and molecular recognition of cyclic ureas. J. Med. Chem. 1996, 39, 3514-3525.
    • Lam, P. Y.; Ru, Y.; Jadhav, P. K.; Aldrich, P. E.; DeLucca, G. V.; Eyermann, C. J.; Chang, C. H.; Emmett, G.; Holler, E. R.; Daneker, W. F.; Li, L.; Confalone, P. N.; McHugh, R. J.; Han, Q.; Li, R.; Markwalder, J. A.; Seitz, S. P.; Sharpe, T. R.; Bacheler, L. T.; Rayner, M. M.; Klabe, R. M.; Shum, L.; Winslow, D. L.; Kornhauser, D. M.; Hodge, C. N. et al. Cyclic HIV protease inhibitors: synthesis, conformational analysis, P2/P2′ structure-activity relationship, and molecular recognition of cyclic ureas. J. Med. Chem. 1996, 39, 3514-3525.
  • 57
    • 0034100511 scopus 로고    scopus 로고
    • Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at Pl
    • Krishnan, R.; Mochalkin, I.; Ami, R.; Tulinsky, A. Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at Pl. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2000, 56, 294-303.
    • (2000) Acta Crystallogr., Sect. D: Biol. Crystallogr , vol.56 , pp. 294-303
    • Krishnan, R.1    Mochalkin, I.2    Ami, R.3    Tulinsky, A.4
  • 59
    • 0025837452 scopus 로고
    • Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors
    • Banner, D. W.; Hadváry, P. Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors. J. Biol. Chem. 1991, 266, 20085-20093.
    • (1991) J. Biol. Chem , vol.266 , pp. 20085-20093
    • Banner, D.W.1    Hadváry, P.2
  • 62
    • 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
  • 63
    • 41549152835 scopus 로고    scopus 로고
    • FlexX, version 1.2; BioSolveIT: Sankt Augustin, Germany
    • FlexX, version 1.2; BioSolveIT: Sankt Augustin, Germany.
  • 64
    • 41549100432 scopus 로고    scopus 로고
    • Sybyl, version 7.1; Tripos, Inc, St. Louis, MO, 2005
    • Sybyl, version 7.1; Tripos, Inc.: St. Louis, MO, 2005.
  • 65
    • 0025829331 scopus 로고
    • Structure at 2.5-a Resolution of Chemically Synthesized Human-Immunodeficiency-Virus Type-1 Protease Complexed with a Hydroxyethylene-Based Inhibitor
    • Jaskolski, M.; Tomasselli, A. G.; Sawyer, T. K.; Staples, D. G.; Heinrikson, R. L. et al. Structure at 2.5-a Resolution of Chemically Synthesized Human-Immunodeficiency-Virus Type-1 Protease Complexed with a Hydroxyethylene-Based Inhibitor. Biochemistry 1991, 30, 1600-1609.
    • (1991) Biochemistry , vol.30 , pp. 1600-1609
    • Jaskolski, M.1    Tomasselli, A.G.2    Sawyer, T.K.3    Staples, D.G.4    Heinrikson, R.L.5
  • 66
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
    • (1997) J. Comput.-Aided Mol. Des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 67
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.
    • (1992) J. Comput. Chem , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 68
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willett, P.; Glen, G. 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, G.3
  • 69
    • 0033545622 scopus 로고    scopus 로고
    • A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach
    • Muegge, I.; Martin, Y. C. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 70
    • 0002535204 scopus 로고
    • Self-organizing neural networks for visualization and classification
    • Opitz, O, Lausen, B, Klar, R, Eds, Springer: Berlin
    • Ultsch, A., Self-organizing neural networks for visualization and classification. In Information and Classification; Opitz, O., Lausen, B., Klar, R., Eds.; Springer: Berlin, 1993; pp 307-313.
    • (1993) Information and Classification , pp. 307-313
    • Ultsch, A.1
  • 71
    • 33745890364 scopus 로고    scopus 로고
    • ESOM-Maps: Tools for clustering, visualization, and classification with Emergent SOM
    • University of Marburg: Germany
    • Ultsch, A.; Moerchen, F. ESOM-Maps: tools for clustering, visualization, and classification with Emergent SOM. In Technical Report Dept. of Mathematics and Computer Science; University of Marburg: Germany, 2005; pp 46-53.
    • (2005) Technical Report Dept. of Mathematics and Computer Science , pp. 46-53
    • Ultsch, A.1    Moerchen, F.2
  • 73
    • 41549156364 scopus 로고    scopus 로고
    • Pipeline Pilot, version 6.0; Accelrys Inc, San Diego, CA
    • Pipeline Pilot, version 6.0; Accelrys Inc.: San Diego, CA.
  • 75
    • 33745686155 scopus 로고    scopus 로고
    • Multifingerprint based similarity searches for targeted class compound selection
    • Kogej, T.; Engkvist, O.; Blomberg, N.; Muresan, S. Multifingerprint based similarity searches for targeted class compound selection. J. Chem. Inf. Model. 2006, 46, 1201-1213.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1201-1213
    • Kogej, T.1    Engkvist, O.2    Blomberg, N.3    Muresan, S.4
  • 76
    • 0041903760 scopus 로고    scopus 로고
    • Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme
    • Xue, L.; Godden, J. W.; Stahura, F. L.; Bajorath, J. Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme. J. Chem. Inf. Comput. Sci. 2003, 43, 1151-1157.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 1151-1157
    • Xue, L.1    Godden, J.W.2    Stahura, F.L.3    Bajorath, J.4
  • 77
    • 28944454140 scopus 로고    scopus 로고
    • Anatomy of fingerprint search calculations on structurally diverse sets of active compounds
    • Godden, J. W.; Stahura, F. L.; Bajorath, J. Anatomy of fingerprint search calculations on structurally diverse sets of active compounds. J. Chem. Inf. Model. 2005, 45, 1812-1819.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1812-1819
    • Godden, J.W.1    Stahura, F.L.2    Bajorath, J.3


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