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Volumn 5, Issue 1, 2009, Pages 56-68

Computational intelligence methods for docking scores

Author keywords

Artificial neural networks; Computational intelligence; Docking scores; Evolutionary algorithms; Fuzzy logic; High throughput screening; In silico docking; Virtual screening

Indexed keywords

BINDING ENERGY; COMPUTER CIRCUITS; FUZZY INFERENCE; FUZZY NEURAL NETWORKS;

EID: 65749110436     PISSN: 15734099     EISSN: None     Source Type: Journal    
DOI: 10.2174/157340909787580863     Document Type: Review
Times cited : (35)

References (200)
  • 1
    • 34548324706 scopus 로고    scopus 로고
    • The cost of biopharmaceutical R&D: Is biotech different?
    • DiMasi, J.A.; Grabowski, H.G. The cost of biopharmaceutical R&D: Is biotech different? Managerial Dec. Econ., 2007, 28, 469-479.
    • (2007) Managerial Dec. Econ , vol.28 , pp. 469-479
    • DiMasi, J.A.1    Grabowski, H.G.2
  • 2
    • 65749102941 scopus 로고    scopus 로고
    • PhRMA Industry Profile 2008 Report, http://www.phrma.org/publications
    • PhRMA Industry Profile 2008 Report, http://www.phrma.org/publications
  • 3
    • 65749097979 scopus 로고    scopus 로고
    • Center for Drug Evaluation and Research: Http://www.fda.gov/cder/rdmt
  • 4
    • 32444441360 scopus 로고    scopus 로고
    • Computational chemistry-driven decision making in lead generation
    • Schnecke, V.; Boström, J. Computational chemistry-driven decision making in lead generation. Drug Discov. Today, 2006, 11, 43-50.
    • (2006) Drug Discov. Today , vol.11 , pp. 43-50
    • Schnecke, V.1    Boström, J.2
  • 5
    • 0034581968 scopus 로고    scopus 로고
    • High-throughput and virtual. screening: Core lead discovery technologies move towards integration
    • Good, A.C.; Krystek, S.R.; Mason, J.S. High-throughput and virtual. screening: Core lead discovery technologies move towards integration. Drug Discov. Today, 2000, 5, S61-S69.
    • (2000) Drug Discov. Today , vol.5
    • Good, A.C.1    Krystek, S.R.2    Mason, J.S.3
  • 6
    • 33645204379 scopus 로고    scopus 로고
    • The design and docking of virtual compound libraries to structure of drug targets
    • Anderson, A.C.; Wright, D.L. The design and docking of virtual compound libraries to structure of drug targets. Curr. Comput. Aided Drug Des., 2005, 1, 103-127.
    • (2005) Curr. Comput. Aided Drug Des , vol.1 , pp. 103-127
    • Anderson, A.C.1    Wright, D.L.2
  • 7
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25.
    • (1997) Adv. Drug Deliv. Rev , vol.23 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 8
    • 42749090651 scopus 로고    scopus 로고
    • Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering
    • Muthas, D.; Sabnis, Y.A.; Lundborg, M.; Karlén, A. Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering. J. Mol. Graphics Model., 2008, 26, 1237-1251.
    • (2008) J. Mol. Graphics Model , vol.26 , pp. 1237-1251
    • Muthas, D.1    Sabnis, Y.A.2    Lundborg, M.3    Karlén, A.4
  • 9
    • 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. Nature Rev. Drug Discov., 2004, 3, 935-949.
    • (2004) Nature Rev. Drug Discov , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 10
    • 0033662998 scopus 로고    scopus 로고
    • Similarity vs docking in 3D virtual screening
    • Mestres, J.; Knegtel, R.M.A. Similarity vs docking in 3D virtual screening. Persp. Drug Discov. Des., 2000, 20, 191.
    • (2000) Persp. Drug Discov. Des , vol.20 , pp. 191
    • Mestres, J.1    Knegtel, R.M.A.2
  • 11
    • 41349090342 scopus 로고    scopus 로고
    • Can we use docking and scoring for hit-to-lead optimization?
    • Enyedy, I.J.; Egan, W.J. Can we use docking and scoring for hit-to-lead optimization? J. Comput. Aided. Mol. Des., 2008, 28, 161-168.
    • (2008) J. Comput. Aided. Mol. Des , vol.28 , pp. 161-168
    • Enyedy, I.J.1    Egan, W.J.2
  • 12
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
    • Leach, A.R.; Shoichet, B.K.; Peishoff, C.E. Prediction of protein-ligand 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
  • 14
    • 40349087133 scopus 로고    scopus 로고
    • Towards the development of universal, fast and highly accurate docking/ scoring methods: A long way to go
    • Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; and Corbeil, C.R. Towards the development of universal, fast and highly accurate docking/ scoring methods: A long way to go. Br. J. Pharmacol., 2008, 153, S7-S26.
    • (2008) Br. J. Pharmacol , vol.153
    • Moitessier, N.1    Englebienne, P.2    Lee, D.3    Lawandi, J.4    Corbeil, C.R.5
  • 15
    • 34249846647 scopus 로고    scopus 로고
    • Artificial Intelligence Approaches for Rational Drug Design and Discovery
    • Duch, W.; Swaminathan, K.; Meller, J. Artificial Intelligence Approaches for Rational Drug Design and Discovery. Curr. Pharm. Des., 2007, 13, 1497-1508.
    • (2007) Curr. Pharm. Des , vol.13 , pp. 1497-1508
    • Duch, W.1    Swaminathan, K.2    Meller, J.3
  • 21
    • 0036606483 scopus 로고    scopus 로고
    • Principles of Docking: An Overviewof Search Algorithms and a Guide to Scoring Functions
    • Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Principles of Docking: An Overviewof Search Algorithms and a Guide to Scoring Functions. Proteins: Struc. Func. Genet., 2002, 47, 409-443.
    • (2002) Proteins: Struc. Func. Genet , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 22
    • 33947536095 scopus 로고    scopus 로고
    • In Silico screening of ligand databases: Methods and applications
    • Khedkar, S.A.; Malde, A.K.; Coutinho, E.C. In Silico screening of ligand databases: Methods and applications. Ind. J. Pharmaceut. Sci., 2008, 68, 689-696.
    • (2008) Ind. J. Pharmaceut. Sci , vol.68 , pp. 689-696
    • Khedkar, S.A.1    Malde, A.K.2    Coutinho, E.C.3
  • 24
    • 84892166712 scopus 로고
    • Einfluss der configuration auf die wirkung der enzyme.
    • Fischer, E. Einfluss der configuration auf die wirkung der enzyme. Ber. 1894, 27, 2985-2993.
    • (1894) Ber , vol.27 , pp. 2985-2993
    • Fischer, E.1
  • 25
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland, D.E. Jr. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA, 1958, 44, 98-104.
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland Jr., D.E.1
  • 26
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J; Milstein C. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA, 1994, 91, 10370-7435.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 10370-17435
    • Foote, J.1    Milstein, C.2
  • 27
    • 33749449880 scopus 로고    scopus 로고
    • Docking and Scoring - Theoretically Easy, Practically Impossible?
    • Coupez, B.; Lewis, R.A. Docking and Scoring - Theoretically Easy, Practically Impossible? Curr. Med. Chem., 2006, 13, 2995-3003.
    • (2006) Curr. Med. Chem , vol.13 , pp. 2995-3003
    • Coupez, B.1    Lewis, R.A.2
  • 28
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • McGovern, S.L.; Shoichet, B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem., 2003, 46, 2895-2907.
    • (2003) J. Med. Chem , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 29
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson, J.A.; Jalaie, M.; Robertson, D.H.; Lewis, R.A.; Vieth, M. Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem., 2004, 47, 45-55.
    • (2004) J. Med. Chem , vol.47 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 30
    • 0037235663 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
    • Bissantz, C.; Bernard, P.; Hibert, M.; Rognan, D. Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets? Proteins, 2003, 50, 5-25.
    • (2003) Proteins , vol.50 , pp. 5-25
    • Bissantz, C.1    Bernard, P.2    Hibert, M.3    Rognan, D.4
  • 31
    • 33645218742 scopus 로고    scopus 로고
    • High-throughput screening of biocatalytic activity: Applications in drug discovery
    • Kumar, R.A.; Clark, D.S. High-throughput screening of biocatalytic activity: Applications in drug discovery. Curr. Opin. Chem. Biol., 2006, 10, 162-168.
    • (2006) Curr. Opin. Chem. Biol , vol.10 , pp. 162-168
    • Kumar, R.A.1    Clark, D.S.2
  • 32
    • 0001971367 scopus 로고
    • The nature of the intermolecular forces operative in biological processes
    • Pauling L.; Delbrück M. The nature of the intermolecular forces operative in biological processes. Science, 1940, 92, 77-79.
    • (1940) Science , vol.92 , pp. 77-79
    • Pauling, L.1    Delbrück, M.2
  • 33
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem., 1959, 14, 1-63.
    • (1959) Adv. Protein Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 35
    • 65749092614 scopus 로고    scopus 로고
    • Hecht, D.; Rios-Reyes, E. Data presented at 29th West Coast Biological Sciences Undergraduate Research Symposium at Point Loma Nazarene University in 2006.
    • Hecht, D.; Rios-Reyes, E. Data presented at 29th West Coast Biological Sciences Undergraduate Research Symposium at Point Loma Nazarene University in 2006.
  • 36
    • 0026813925 scopus 로고
    • The Computer Program Ludi: A New Method for the de Novo Design of Enzyme Inhibitors
    • Böhm H.J. The Computer Program Ludi: A New Method for the de Novo Design of Enzyme Inhibitors. J. Comput. Aided. Mol. Des. 1992, 6, 61-78.
    • (1992) J. Comput. Aided. Mol. Des , vol.6 , pp. 61-78
    • Böhm, H.J.1
  • 37
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional sturcture
    • Böhm H.J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional sturcture. J. Comput. Aided Mol. Des., 1994, 8, 243.
    • (1994) J. Comput. Aided Mol. Des , vol.8 , pp. 243
    • Böhm, H.J.1
  • 38
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G.M.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R.K.; Olsen, A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem., 1998, 9, 1639-1662.
    • (1998) J. Comput. Chem , vol.9 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olsen, A.J.7
  • 39
    • 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
  • 41
    • 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
  • 44
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • Jain, A.N. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J. Comput. Aided. Mol. Des., 1996, 10, 427-440.
    • (1996) J. Comput. Aided. Mol. Des , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 45
    • 0037030649 scopus 로고    scopus 로고
    • Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. models without explicit constrained water
    • Cozzini P.; Fornabaio M.; Marabotti A.; Abraham D.J.; Kellogg G.E.; Mozzarelli A. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. models without explicit constrained water. J. Med. Chem., 2002, 45, 2469-2483.
    • (2002) J. Med. Chem , vol.45 , pp. 2469-2483
    • Cozzini, P.1    Fornabaio, M.2    Marabotti, A.3    Abraham, D.J.4    Kellogg, G.E.5    Mozzarelli, A.6
  • 46
    • 15244346501 scopus 로고    scopus 로고
    • Krammer, A.; Kirchhoff, P.D.; Jiang, X.; Venkatachalam, C.M.; Waldman, M. LigScore: A novel scoring function for predicting binding affinities. J. Mol. Graph. Model., 2005, 23, 395-407.
    • Krammer, A.; Kirchhoff, P.D.; Jiang, X.; Venkatachalam, C.M.; Waldman, M. LigScore: A novel scoring function for predicting binding affinities. J. Mol. Graph. Model., 2005, 23, 395-407.
  • 47
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar D.K.; Verkhivker G.M.; Rejto P.A.; Sherman C.J.; Fogel D.B.; Fogel, L.J.; Freer, S.T. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming. Chem. Biol., 1995, 2, 317-24.
    • (1995) Chem. Biol , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 48
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang R.; Liu L.; Lai L.; Tang Y. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Mod., 1998, 4, 379-394.
    • (1998) J. Mol. Mod , vol.4 , pp. 379-394
    • Wang, R.1    Liu, L.2    Lai, L.3    Tang, Y.4
  • 49
    • 33644843080 scopus 로고    scopus 로고
    • PSI-DOCK: Towards highly efficient and accurate flexible ligand docking
    • Pei J.; Wang Q.; Liu Z.; Li Q.; Yang K.; Lai L. PSI-DOCK: Towards highly efficient and accurate flexible ligand docking. Proteins Struct. Funct. Genet., 2006, 62, 934-946.
    • (2006) Proteins Struct. Funct. Genet , vol.62 , pp. 934-946
    • Pei, J.1    Wang, Q.2    Liu, Z.3    Li, Q.4    Yang, K.5    Lai, L.6
  • 50
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • Stahl M.; Rarey M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44, 1035-1042.
    • (2001) J. Med. Chem , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 52
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang R.; Lai L.;Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided. Mol. Des., 2002, 16, 11-26.
    • (2002) J. Comput. Aided. Mol. Des , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 55
    • 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
  • 56
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
    • Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins, 1999, 37, 228-241.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 57
    • 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
  • 58
    • 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
  • 59
    • 84986522918 scopus 로고
    • ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R.; Totrov M.; Kuznetsov D. ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem., 1994, 15, 488-506.
    • (1994) J. Comput. Chem , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 60
    • 0031181346 scopus 로고    scopus 로고
    • Powerful, rapid computer algorithms for structure-based drug design
    • McMartin C.; Bohacek R.S. QXP: Powerful, rapid computer algorithms for structure-based drug design. J. Comput. Aided. Mol. Des., 1997, 11, 333-344.
    • (1997) J. Comput. Aided. Mol. Des , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.Q.2
  • 61
    • 33749266178 scopus 로고    scopus 로고
    • A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptide and pseudopeptidic β-secretase (BACE 1) inhibitors
    • Moitessier N.; Therrien E.; Hanessian S. A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptide and pseudopeptidic β-secretase (BACE 1) inhibitors. J. Med. Chem., 2006, 49, 5885-5894.
    • (2006) J. Med. Chem , vol.49 , pp. 5885-5894
    • Moitessier, N.1    Therrien, E.2    Hanessian, S.3
  • 62
    • 0029995624 scopus 로고    scopus 로고
    • A new method for the receptor-based prediction of binding affinities of novel ligands
    • Head, R.D.; Smythe, M.L.; Oprea, T.I.; Waller, C.L.; Green, S.M.; Marshall, G.R. A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc., 1996, 118, 3959-3969.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 63
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol., 2000, i 295, 337-356.
    • (2000) J. Mol. Biol , vol.1 , Issue.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 64
    • 26444588137 scopus 로고    scopus 로고
    • DrugScore(CSD)-Knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
    • Velec, H.F.G.; Gohlke, H.; Klebe, G. DrugScore(CSD)-Knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J. Med. Chem., 2005, 48, 6296-6303.
    • (2005) J. Med. Chem , vol.48 , pp. 6296-6303
    • Velec, H.F.G.1    Gohlke, H.2    Klebe, G.3
  • 65
    • 0000882405 scopus 로고    scopus 로고
    • BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
    • Mitchell, J.B.O.; Laskowski R.A.; Alex A.; Forster M.J.; Thornton, J. BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data J. Comput. Chem. 1999, 20, 1177-1185.
    • (1999) J. Comput. Chem , vol.20 , pp. 1177-1185
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Forster, M.J.4    Thornton, J.5
  • 66
    • 33749239216 scopus 로고    scopus 로고
    • A new knowledge-based potential scoring function accounting for protein atom mobility
    • Yang C.Y.; Wang, R.; Wang, S. M-Score: A new knowledge-based potential scoring function accounting for protein atom mobility. J. Med. Chem., 2006, 49, 5903-5911.
    • (2006) J. Med. Chem , vol.49 , pp. 5903-5911
    • Yang, C.Y.1    Wang, R.2    Wang3    M-Score, S.4
  • 67
    • 0031717170 scopus 로고    scopus 로고
    • Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
    • Schaffer, L.; Verkhivker, G.M. Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins, 1998, 33, 295-310.
    • (1998) Proteins , vol.33 , pp. 295-310
    • Schaffer, L.1    Verkhivker, G.M.2
  • 68
    • 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
  • 69
    • 0033673508 scopus 로고    scopus 로고
    • A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
    • Muegge, I. A knowledge-based scoring function for protein-ligand interactions: Probing the reference state. Perspect. Drug Discov. Des., 2000, 20, 99-114.
    • (2000) Perspect. Drug Discov. Des , vol.20 , pp. 99-114
    • Muegge, I.1
  • 70
    • 0001745748 scopus 로고    scopus 로고
    • Effect of ligand volume correction on PMF scoring
    • Muegge, I. Effect of ligand volume correction on PMF scoring. J. Comput. Chem., 2001, 22, 418-425.
    • (2001) J. Comput. Chem , vol.22 , pp. 418-425
    • Muegge, I.1
  • 71
    • 33846487854 scopus 로고    scopus 로고
    • Muegge, I.; Oloff, S. Advances in virtual screening. Drug Discov. Today Technol., 2006, 3, 405-411.
    • Muegge, I.; Oloff, S. Advances in virtual screening. Drug Discov. Today Technol., 2006, 3, 405-411.
  • 72
    • 0000934205 scopus 로고    scopus 로고
    • SMoG: De Novo design method based on simple, fast, and accurate free energy estimates. 1. methodology and supporting evidence
    • DeWitte, R. S.; Shakhnovich, E.I. SMoG: De Novo design method based on simple, fast, and accurate free energy estimates. 1. methodology and supporting evidence. J. Am.Chem. Soc., 1996, 118, 11733-11744.
    • (1996) J. Am.Chem. Soc , vol.118 , pp. 11733-11744
    • DeWitte, R.S.1    Shakhnovich, E.I.2
  • 73
    • 0037142298 scopus 로고    scopus 로고
    • Small molecule growth 2001 (SmoG2001): An improved knowledge-based Scoring function for protein-ligand interactions
    • Ishchenko, A.V.; Shakhnovich, E.I. Small molecule growth 2001 (SmoG2001): An improved knowledge-based Scoring function for protein-ligand interactions. J. Med. Chem., 2002, 45, 2770-2780.
    • (2002) J. Med. Chem , vol.45 , pp. 2770-2780
    • Ishchenko, A.V.1    Shakhnovich, E.I.2
  • 75
    • 0031135364 scopus 로고    scopus 로고
    • A comparison of heuristic search algorithms for molecular docking
    • Westhead, D.R.; Clark, D.E.; Murray, C.W. A comparison of heuristic search algorithms for molecular docking. J. Comput. Aided. Mol. Des., 1997, 11, 209-228.
    • (1997) J. Comput. Aided. Mol. Des , vol.11 , pp. 209-228
    • Westhead, D.R.1    Clark, D.E.2    Murray, C.W.3
  • 76
    • 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
  • 77
    • 0035829446 scopus 로고    scopus 로고
    • Evaluation of scoring functions for protein-ligand docking
    • Perez, C.; Ortiz, A.R. Evaluation of scoring functions for protein-ligand docking. J. Med. Chem., 2001, 44, 3768-3785.
    • (2001) J. Med. Chem , vol.44 , pp. 3768-3785
    • Perez, C.1    Ortiz, A.R.2
  • 78
    • 0035811458 scopus 로고    scopus 로고
    • A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities
    • Terp, G.E.; Johansen, B.N.; Christensen, I.T.; Jørgensen, F.S. A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. J. Med. Chem., 2001, 44, 2333-2343.
    • (2001) J. Med. Chem , vol.44 , pp. 2333-2343
    • Terp, G.E.1    Johansen, B.N.2    Christensen, I.T.3    Jørgensen, F.S.4
  • 79
    • 0142028937 scopus 로고    scopus 로고
    • Kinases, homology models, and high throughput docking
    • Diller, D.J.; Li, R. Kinases, homology models, and high throughput docking. J. Med. Chem., 2003, 46, 4638-4647.
    • (2003) J. Med. Chem , vol.46 , pp. 4638-4647
    • Diller, D.J.1    Li, R.2
  • 80
    • 0037235881 scopus 로고    scopus 로고
    • Virtual screening to enrich hit lists from high-throughput screening: A case study on small-molecule inhibitors of angiogenin
    • Jenkins, J.L.; Kao, R.Y.T; Shapiro, R. Virtual screening to enrich hit lists from high-throughput screening: A case study on small-molecule inhibitors of angiogenin. Proteins Struct. Funct. Genet., 2003, 50, 81-93.
    • (2003) Proteins Struct. Funct. Genet , vol.50 , pp. 81-93
    • Jenkins, J.L.1    Kao, R.Y.T.2    Shapiro, R.3
  • 81
    • 0038185582 scopus 로고    scopus 로고
    • Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools
    • Schulz-Gasch, T.; Stahl, M. Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools. J. Mol. Mod., 2003, 9, 47-57.
    • (2003) J. Mol. Mod , vol.9 , pp. 47-57
    • Schulz-Gasch, T.1    Stahl, M.2
  • 82
    • 0037763817 scopus 로고    scopus 로고
    • Comparative Evaluation of 11 Scoring Functions for Molecular Docking
    • Wang, R.; Lu, Y.; Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J. Med. Chem., 2003, 46, 2287-2303.
    • (2003) J. Med. Chem , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 83
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • Wang, R.; Lu, Y.; Fang, X.; Wang, S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci., 2004, 44, 2114-2125.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 2114-2125
    • Wang, R.1    Lu, Y.2    Fang, X.3    Wang, S.4
  • 85
    • 4544367743 scopus 로고    scopus 로고
    • Comparative evaluation of eight docking tools for docking and virtual screening
    • Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. Comparative evaluation of eight docking tools for docking and virtual screening. Proteins Struct. Funct. Genet., 2004, 57, 225-242.
    • (2004) Proteins Struct. Funct. Genet , vol.57 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4
  • 86
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • Kontoyianni, M.; McClellan, L.M.; Sokol, G.S. Evaluation of docking performance: Comparative data on docking algorithms. J. Med. Chem., 2004, 47, 558-565.
    • (2004) J. Med. Chem , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 88
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola, E.; Walters, W.P.; Charifson, P.S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins Struct. Funct. Genet., 2004, 56, 235-249.
    • (2004) Proteins Struct. Funct. Genet , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 89
    • 33244483907 scopus 로고    scopus 로고
    • On evaluating molecular-docking methods for pose prediction and enrichment factors
    • Chen, H.; Lyne, P.D.; Giordanetto, F.; Lovell, T.; Li, J. On evaluating molecular-docking methods for pose prediction and enrichment factors J. Chem. Inf. Model., 2006, 46 401-415.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 401-415
    • Chen, H.1    Lyne, P.D.2    Giordanetto, F.3    Lovell, T.4    Li, J.5
  • 92
    • 34547661861 scopus 로고    scopus 로고
    • Comparative performance of several flexible docking programs and scoring functions: Fnrichment dtudies for a diverse set of pharmaceutically relevant targets
    • Zhou, Z.; Felts, A.K.; Friesner, R.A.; Levy, R.M. Comparative performance of several flexible docking programs and scoring functions: fnrichment dtudies for a diverse set of pharmaceutically relevant targets. J. Chem. Inf. Model., 2007, 47, 1599-1608.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1599-1608
    • Zhou, Z.1    Felts, A.K.2    Friesner, R.A.3    Levy, R.M.4
  • 93
    • 34247260419 scopus 로고    scopus 로고
    • Comments on the article On evaluating molecular-docking methods for pose prediction and enrichment factors
    • Perola E.; Walters W.P.; Charifson P. Comments on the article "On evaluating molecular-docking methods for pose prediction and enrichment factors." J. Chem. Inf. Model., 2007, 47, 251-253.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 251-253
    • Perola, E.1    Walters, W.P.2    Charifson, P.3
  • 94
    • 41349106585 scopus 로고    scopus 로고
    • Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
    • Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes? J. Comput. Aided Mol. Des., 2008, 22, 213-228.
    • (2008) J. Comput. Aided Mol. Des , vol.22 , pp. 213-228
    • Kirchmair, J.1    Markt, P.2    Distinto, S.3    Wolber, G.4    Langer, T.5
  • 97
    • 34547670476 scopus 로고    scopus 로고
    • Evaluations of molecular docking programs for virtual screening
    • Onodera K.; Satou K.; Hirota H. Evaluations of molecular docking programs for virtual screening. J. Chem. Inf. Model. 2007, 47, 1609-1618.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1609-1618
    • Onodera, K.1    Satou, K.2    Hirota, H.3
  • 99
    • 34248562742 scopus 로고    scopus 로고
    • Grosdidier A.; Zoete V.; Michielin, O. EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins Struct. Funct. Genet., 2007, 67, 1010-1025.
    • Grosdidier A.; Zoete V.; Michielin, O. EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization. Proteins Struct. Funct. Genet., 2007, 67, 1010-1025.
  • 100
    • 34548200847 scopus 로고    scopus 로고
    • Structure-based drug design: Docking and dcoring
    • Kroemer, R.T. Structure-based drug design: Docking and dcoring. Curr. Protein Pept. Sci., 2007, 8, 312-328.
    • (2007) Curr. Protein Pept. Sci , vol.8 , pp. 312-328
    • Kroemer, R.T.1
  • 101
    • 3342933156 scopus 로고    scopus 로고
    • Target-biased scoring approaches and expert systems in structure-based virtual screening
    • Jansen, J.M.; Martin, E.J. Target-biased scoring approaches and expert systems in structure-based virtual screening. Curr. Opin. Chem. Biol., 2004, 8, 359-364.
    • (2004) Curr. Opin. Chem. Biol , vol.8 , pp. 359-364
    • Jansen, J.M.1    Martin, E.J.2
  • 102
    • 38649091945 scopus 로고    scopus 로고
    • Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
    • Fogel, G.B.; Cheung, M.;Pittman, E.; Hecht, D. Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives. J. Comput. Aided. Mol. Des., 2008, 22, 29-38.
    • (2008) J. Comput. Aided. Mol. Des , vol.22 , pp. 29-38
    • Fogel, G.B.1    Cheung, M.2    Pittman, E.3    Hecht, D.4
  • 103
    • 33744826819 scopus 로고    scopus 로고
    • MolDock: A new technique for high-accuracy molecular docking
    • Thomsen R.; Christensen M.H. MolDock: A new technique for high-accuracy molecular docking. J. Med. Chem., 2006, 49, 3315-3321.
    • (2006) J. Med. Chem , vol.49 , pp. 3315-3321
    • Thomsen, R.1    Christensen, M.H.2
  • 104
    • 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
  • 105
    • 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.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1134
    • Yang, J.M.1    Chen, Y.F.2    Shen, T.W.3    Kristal, B.S.4    Hsu, D.F.5
  • 106
    • 45949096079 scopus 로고    scopus 로고
    • Computational intelligence approaches for pattern discovery in biological systems
    • Fogel, G.B. Computational intelligence approaches for pattern discovery in biological systems. Brief Bioinform., 2008, 9, 307-316.
    • (2008) Brief Bioinform , vol.9 , pp. 307-316
    • Fogel, G.B.1
  • 107
    • 0035860537 scopus 로고    scopus 로고
    • Machine learning for science: State of the art and future prospects
    • Mjolsness E; DeCoste D. Machine learning for science: State of the art and future prospects. Science, 2001, 293, 2051-5.
    • (2001) Science , vol.293 , pp. 2051-2055
    • Mjolsness, E.1    DeCoste, D.2
  • 108
    • 0242677271 scopus 로고
    • A quantitative approach to biochemical structure-activity relationships
    • Hansch, C. A quantitative approach to biochemical structure-activity relationships. Acc.Chem. Res., 1969, 2, 232-239.
    • (1969) Acc.Chem. Res , vol.2 , pp. 232-239
    • Hansch, C.1
  • 110
    • 0035272009 scopus 로고    scopus 로고
    • A quantum mechanical/neural net model for boiling points with error estimation
    • Chalk, A.J.; Beck, B.; Clark, T. A quantum mechanical/neural net model for boiling points with error estimation. J. Chem. Inf. Comput. Sci., 2001, 41, 457-462.
    • (2001) J. Chem. Inf. Comput. Sci , vol.41 , pp. 457-462
    • Chalk, A.J.1    Beck, B.2    Clark, T.3
  • 111
    • 18344410789 scopus 로고    scopus 로고
    • Toward generating simpler QSAR models: Non-linear multivariate regression vs several neural network ensembles and some related methods
    • Lučić, B.; Nadramija, D.; Bašic, I.; Tranajstić, N. Toward generating simpler QSAR models: Non-linear multivariate regression vs several neural network ensembles and some related methods. J. Chem. Inf. Comput. Sci., 2003, 43, 1094-1102.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 1094-1102
    • Lučić, B.1    Nadramija, D.2    Bašic, I.3    Tranajstić, N.4
  • 112
    • 0037352051 scopus 로고    scopus 로고
    • Prediction of dihydrofolate reductase inhibition and selectivity using computational neural networks and linear discriminant analysis
    • Mattioni, B.E.; Jurs, P.C. Prediction of dihydrofolate reductase inhibition and selectivity using computational neural networks and linear discriminant analysis. J. Mol. Graphics Model., 2003, 21, 391-419.
    • (2003) J. Mol. Graphics Model , vol.21 , pp. 391-419
    • Mattioni, B.E.1    Jurs, P.C.2
  • 113
    • 0345724883 scopus 로고    scopus 로고
    • Evolutionary optimization, backpropagation, and data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives
    • Weekes, D.; Fogel, G.B. Evolutionary optimization, backpropagation, and data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives. Biosystems, 2003, 72, 149-158.
    • (2003) Biosystems , vol.72 , pp. 149-158
    • Weekes, D.1    Fogel, G.B.2
  • 114
    • 2942538155 scopus 로고    scopus 로고
    • Modelling blood-brain barrier partitioning using Bayesian neural nets
    • Winkler, D.A.; Burden, F.R. Modelling blood-brain barrier partitioning using Bayesian neural nets. J. Mol. Graph. Model., 2004, 22, 499-505.
    • (2004) J. Mol. Graph. Model , vol.22 , pp. 499-505
    • Winkler, D.A.1    Burden, F.R.2
  • 115
    • 14944350238 scopus 로고    scopus 로고
    • A general method for exploiting QSAR models in lead optimization
    • Lewis, R.A. A general method for exploiting QSAR models in lead optimization. J. Med. Chem. 2005, 48, 1638-1648.
    • (2005) J. Med. Chem , vol.48 , pp. 1638-1648
    • Lewis, R.A.1
  • 116
    • 33750321101 scopus 로고    scopus 로고
    • Novel approaches for small biomolecule classification and structural similarity search
    • Karakoc, E.; Sahinalp, S.C.; Cherkasov, A. Novel approaches for small biomolecule classification and structural similarity search. J. Chem. Inf. Model., 2006, 46, 2167-2182.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2167-2182
    • Karakoc, E.1    Sahinalp, S.C.2    Cherkasov, A.3
  • 117
    • 0023751431 scopus 로고
    • Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
    • Cramer III, R.D.; Patterson, D.E.; Bunce, J.D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110, 5959-5967.
    • (1988) J. Am. Chem. Soc , vol.110 , pp. 5959-5967
    • Cramer III, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 118
    • 0027944195 scopus 로고
    • Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
    • Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem., 1994, 37, 4130-4146.
    • (1994) J. Med. Chem , vol.37 , pp. 4130-4146
    • Klebe, G.1    Abraham, U.2    Mietzner, T.3
  • 119
    • 51249194645 scopus 로고
    • A logical calculus of the ideas immanent in nervous activity
    • McCulloch, W.S., Pitts, W. A logical calculus of the ideas immanent in nervous activity. Bull. Math Biophys., 1943, 5, 115-133.
    • (1943) Bull. Math Biophys , vol.5 , pp. 115-133
    • McCulloch, W.S.1    Pitts, W.2
  • 123
    • 34248666540 scopus 로고
    • Fuzzy sets
    • Zadeh, L.A. Fuzzy sets. Inform. Control, 1965, 8, 338-53.
    • (1965) Inform. Control , vol.8 , pp. 338-353
    • Zadeh, L.A.1
  • 124
    • 49949129142 scopus 로고
    • Fuzzy Algorithms
    • Zadeh L.A. Fuzzy Algorithms. Inform. Control, 1968, 12, 94-102.
    • (1968) Inform. Control , vol.12 , pp. 94-102
    • Zadeh, L.A.1
  • 125
    • 33646361042 scopus 로고    scopus 로고
    • Fuzzy logic in medicine and bioinformatics
    • Torres, A.; Nieto, J.J. Fuzzy logic in medicine and bioinformatics. J.Biomed. Biotechnol., 2006, 2, 91908.
    • (2006) J.Biomed. Biotechnol , vol.2 , pp. 91908
    • Torres, A.1    Nieto, J.J.2
  • 129
    • 0003509518 scopus 로고    scopus 로고
    • Ruspini, E.H, Bonissone, P.P, Pedrycz, W. Eds, Bristol, UK: Oxford University Press
    • Ruspini, E.H.; Bonissone, P.P.; Pedrycz, W. Eds.; Handbook of fuzzy computation; Bristol, UK: Oxford University Press, 1998.
    • (1998) Handbook of fuzzy computation
  • 130
    • 34248152046 scopus 로고    scopus 로고
    • Type-2 Fuzzy sets and systems: An overview
    • Mendel, J.M. Type-2 Fuzzy sets and systems: An overview. IEEE Comput. Intell. Mag., 2007, 2, 20-29.
    • (2007) IEEE Comput. Intell. Mag , vol.2 , pp. 20-29
    • Mendel, J.M.1
  • 132
    • 0016458950 scopus 로고
    • The concept of a linguistic variable and its application to approximate reasoning-1
    • Zadeh, L.A. The concept of a linguistic variable and its application to approximate reasoning-1. Inform. Sci., 1975, 8, 199-249.
    • (1975) Inform. Sci , vol.8 , pp. 199-249
    • Zadeh, L.A.1
  • 133
    • 15344339772 scopus 로고    scopus 로고
    • A neuro-fuzzy approach to virtual screening in molecular bioinformatics
    • Paetz, J.; Schneider, G. A neuro-fuzzy approach to virtual screening in molecular bioinformatics. Fuzzy Sets Sys., 2005, 152, 67-82.
    • (2005) Fuzzy Sets Sys , vol.152 , pp. 67-82
    • Paetz, J.1    Schneider, G.2
  • 134
    • 0037424605 scopus 로고    scopus 로고
    • Efficient conformational sampling of local side-chain flexibility
    • Källblad, P.; Dean, P.M. Efficient conformational sampling of local side-chain flexibility. J. Mol. Biol., 2003, 326, 1651-1665.
    • (2003) J. Mol. Biol , vol.326 , pp. 1651-1665
    • Källblad, P.1    Dean, P.M.2
  • 138
    • 65749089166 scopus 로고    scopus 로고
    • Bremmerman, H.J. Optimization through evolution and recombination; Yovits M.C.; Jacobi G.T.; Goldstein G.D. Eds.; Self-organizing systems. Washington DC: Spartan Press, 1962.
    • Bremmerman, H.J. Optimization through evolution and recombination; Yovits M.C.; Jacobi G.T.; Goldstein G.D. Eds.; Self-organizing systems. Washington DC: Spartan Press, 1962.
  • 143
    • 0031122887 scopus 로고    scopus 로고
    • Dorigo, M; Gambardella, L.M. Ant colony system: A cooperative learning approach to the traveling salesman problem. IEEE Trans. Evol. Comput., 1997, 1, 53-66.
    • Dorigo, M; Gambardella, L.M. Ant colony system: A cooperative learning approach to the traveling salesman problem. IEEE Trans. Evol. Comput., 1997, 1, 53-66.
  • 144
    • 0003853519 scopus 로고
    • Differential evolution: A simple and efficient sdaptive scheme for global optimization over continuous spaces
    • Technical report TR-95-012, ICSI, March
    • Storn, R.; Price, K. Differential evolution: A simple and efficient sdaptive scheme for global optimization over continuous spaces. Technical report TR-95-012, ICSI, March 1995.
    • (1995)
    • Storn, R.1    Price, K.2
  • 145
    • 0033115654 scopus 로고    scopus 로고
    • System design by constraint adaptation and differential evolution
    • Storn, R. System design by constraint adaptation and differential evolution. IEEE Trans. Evol. Comput., 1999, 3, 22-34.
    • (1999) IEEE Trans. Evol. Comput , vol.3 , pp. 22-34
    • Storn, R.1
  • 148
    • 0033362601 scopus 로고    scopus 로고
    • Evolving artificial neural networks
    • Yao, X. Evolving artificial neural networks. Proc. IEEE, 1999, 87, 1423-1447.
    • (1999) Proc. IEEE , vol.87 , pp. 1423-1447
    • Yao, X.1
  • 150
    • 34547963127 scopus 로고    scopus 로고
    • High-throughput ligand screening via pre-clustering and rvolved neural networks. IEEE/ACM Trans
    • Hecht, D.; Fogel, G.B. High-throughput ligand screening via pre-clustering and rvolved neural networks. IEEE/ACM Trans. Comput. Biol. Bioinf., 2007, 4, 476-84.
    • (2007) Comput. Biol. Bioinf , vol.4 , pp. 476-484
    • Hecht, D.1    Fogel, G.B.2
  • 151
    • 39949084319 scopus 로고    scopus 로고
    • QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives
    • Hecht, D.; Cheung, M.; Fogel, G.B. QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives. Biosystems 2008, 92, 10-15.
    • (2008) Biosystems , vol.92 , pp. 10-15
    • Hecht, D.1    Cheung, M.2    Fogel, G.B.3
  • 153
    • 0344254815 scopus 로고    scopus 로고
    • Drug discovery using support vector machines. The case studies of drug-likeness, agrochemical-likeness, and enzyme inhibition predictions
    • Zernov, V.V.; Balakin, K.V.; Ivaschenko, A.A.; Nikolay P.; Savchuk, N.P.; Pletnev, I.V. Drug discovery using support vector machines. The case studies of drug-likeness, agrochemical-likeness, and enzyme inhibition predictions. J. Chem. Inf. Comput. Sci., 2003, 43, 2048-2056.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 2048-2056
    • Zernov, V.V.1    Balakin, K.V.2    Ivaschenko, A.A.3    Nikolay, P.4    Savchuk, N.P.5    Pletnev, I.V.6
  • 154
    • 43049157546 scopus 로고    scopus 로고
    • A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor
    • Han, L.Y.; Ma, X.H.; Lin, H.H.; Jia, J.; Zhu, F.; Xuec, Y.; Li, Z.R.; Cao, Z.W.; Ji, Z.L.; Chen, Y.Z. A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor. J. Mol. Graph. Model., 2008, 26, 1276-1286.
    • (2008) J. Mol. Graph. Model , vol.26 , pp. 1276-1286
    • Han, L.Y.1    Ma, X.H.2    Lin, H.H.3    Jia, J.4    Zhu, F.5    Xuec, Y.6    Li, Z.R.7    Cao, Z.W.8    Ji, Z.L.9    Chen, Y.Z.10
  • 155
    • 39749108754 scopus 로고    scopus 로고
    • Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
    • Martin, O.; Schomburg, D. Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines. Proteins, 2008, 70, 1367-1378.
    • (2008) Proteins , vol.70 , pp. 1367-1378
    • Martin, O.1    Schomburg, D.2
  • 157
    • 17644371944 scopus 로고    scopus 로고
    • A support vector machine approach to the identification of phosphorylation sites
    • Plewczynski, D.; Tkacz, A.;Godzik, A.;Rychlewski, L. A support vector machine approach to the identification of phosphorylation sites. Cell. Mol. Biol. Lett., 2005, 10, 73-89.
    • (2005) Cell. Mol. Biol. Lett , vol.10 , pp. 73-89
    • Plewczynski, D.1    Tkacz, A.2    Godzik, A.3    Rychlewski, L.4
  • 158
    • 0000667930 scopus 로고    scopus 로고
    • Training nu-support vector classifiers: Theory and algorithms
    • Chang, C.C.; Lin, C.J. Training nu-support vector classifiers: Theory and algorithms. Neural Comput., 2001, 13, 2119-2147.
    • (2001) Neural Comput , vol.13 , pp. 2119-2147
    • Chang, C.C.1    Lin, C.J.2
  • 159
    • 4143132047 scopus 로고    scopus 로고
    • Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results
    • Klon, A.E.; Glick, M.; Davies, J.W. Combination of a naive Bayes classifier with consensus scoring improves enrichment of high-throughput docking results. J. Med. Chem., 2004, 47, 4356-4359.
    • (2004) J. Med. Chem , vol.47 , pp. 4356-4359
    • Klon, A.E.1    Glick, M.2    Davies, J.W.3
  • 160
    • 2442716437 scopus 로고    scopus 로고
    • Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results
    • Klon, A.E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J.W. Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results. J. Med. Chem., 2004, 47, 2743.
    • (2004) J. Med. Chem , vol.47 , pp. 2743
    • Klon, A.E.1    Glick, M.2    Thoma, M.3    Acklin, P.4    Davies, J.W.5
  • 161
    • 27444445346 scopus 로고    scopus 로고
    • PostDock A structural, empirical approach to scoring protein ligand complexes
    • Springer, C.; Adalsteinsson, H.; Young, M.M.; Kegelmeyer, P.W. Roe, D.C. PostDock A structural, empirical approach to scoring protein ligand complexes. J. Med. Chem., 2005, 48, 6821-6831.
    • (2005) J. Med. Chem , vol.48 , pp. 6821-6831
    • Springer, C.1    Adalsteinsson, H.2    Young, M.M.3    Kegelmeyer, P.W.4    Roe, D.C.5
  • 163
    • 42449142325 scopus 로고    scopus 로고
    • A new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data
    • Pearlman, D.A.; Rao, B.G.; Charifson, P. FURSMASA: A new approach to rapid scoring functions that uses a MD-averaged potential energy grid and a solvent-accessible surface area term with parameters GA fit to experimental data. Proteins, 2008, 71, 1519-1538.
    • (2008) Proteins , vol.71 , pp. 1519-1538
    • Pearlman, D.A.1    Rao, B.G.2    Charifson3    FURSMASA, P.4
  • 164
    • 6044238257 scopus 로고    scopus 로고
    • A docking score function for estimating ligand-protein interactions: Application to acetylcholinesterase inhibition
    • Guo, J.; Hurley, M.M.; Wright, J.B.; Gerald H. Lushington, G.H. A docking score function for estimating ligand-protein interactions: application to acetylcholinesterase inhibition. J. Med. Chem., 2004, 47, 5492-5500.
    • (2004) J. Med. Chem , vol.47 , pp. 5492-5500
    • Guo, J.1    Hurley, M.M.2    Wright, J.B.3    Gerald, H.4    Lushington, G.H.5
  • 165
    • 33846889763 scopus 로고    scopus 로고
    • Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery
    • Catana, C.; Pieter, F.W.; Stouten, P.F.W. Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery. J. Chem. Inf. Model., 2007, 47, 85-91.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 85-91
    • Catana, C.1    Pieter, F.W.2    Stouten, P.F.W.3
  • 166
    • 41549086249 scopus 로고    scopus 로고
    • Supervised scoring models with docked ligand conformations for structure-based virtual screening
    • Teramoto, R.; Fukunishi, H. Supervised scoring models with docked ligand conformations for structure-based virtual screening. J. Chem. Inf. Model., 2008, 48, 288-295.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 288-295
    • Teramoto, R.1    Fukunishi, H.2
  • 168
    • 26944456622 scopus 로고    scopus 로고
    • Knowledge-driven lead discovery
    • Pirard, B. Knowledge-driven lead discovery. Mini Rev. Med. Chem., 2005, 5, 1045-1052.
    • (2005) Mini Rev. Med. Chem , vol.5 , pp. 1045-1052
    • Pirard, B.1
  • 170
    • 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
  • 171
    • 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
  • 172
    • 0037153231 scopus 로고    scopus 로고
    • Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A
    • Cui, M.; Huang, X.; Luo, X.; Briggs, J.M.; Ji, R.; Chen, K.; Shen, J.; Jiang, H. Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A. J. Med. Chem., 2002, 45, 5249-5259.
    • (2002) J. Med. Chem , vol.45 , pp. 5249-5259
    • Cui, M.1    Huang, X.2    Luo, X.3    Briggs, J.M.4    Ji, R.5    Chen, K.6    Shen, J.7    Jiang, H.8
  • 173
    • 0037168053 scopus 로고    scopus 로고
    • Inhibitory mode of 1,5-diarylpyrazole derivatives against cyclooxygenase-2 and cyclooxygenase-1: Molecular docking and 3D QSAR analyses
    • Liu, H.; Huang, X.; Shen, J.; Luo, X.; Li, M.; Xiong, B.; Chen, G.; Shen, J.; Yang, Y.; Jiang, H.; Chen, K. Inhibitory mode of 1,5-diarylpyrazole derivatives against cyclooxygenase-2 and cyclooxygenase-1: Molecular docking and 3D QSAR analyses. J. Med. Chem., 2002, 45, 4816-4827.
    • (2002) J. Med. Chem , vol.45 , pp. 4816-4827
    • Liu, H.1    Huang, X.2    Shen, J.3    Luo, X.4    Li, M.5    Xiong, B.6    Chen, G.7    Shen, J.8    Yang, Y.9    Jiang, H.10    Chen, K.11
  • 174
    • 3042747902 scopus 로고    scopus 로고
    • Inhibitory mode of indole-2-carboxamide derivatives against HLGPa: Molecular docking and 3D-QSAR analyses
    • Liu, G.; Zhang, Z.; Luo, X.; Shen, J.; Liu, H.; Shen, X.; Chen, K.; Jiang, H. Inhibitory mode of indole-2-carboxamide derivatives against HLGPa: Molecular docking and 3D-QSAR analyses. Bioorg. Med. Chem., 2004, 12, 4147-4157.
    • (2004) Bioorg. Med. Chem , vol.12 , pp. 4147-4157
    • Liu, G.1    Zhang, Z.2    Luo, X.3    Shen, J.4    Liu, H.5    Shen, X.6    Chen, K.7    Jiang, H.8
  • 175
    • 26944484425 scopus 로고    scopus 로고
    • Modeling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques
    • Wei, H.-Y.; Tsai, K.-C.; Lin, T.-H. Modeling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques. J. Chem. Inf. Model., 2005, 45, 1343-1351.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1343-1351
    • Wei, H.-Y.1    Tsai, K.-C.2    Lin, T.-H.3
  • 176
    • 13844312018 scopus 로고    scopus 로고
    • Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with β-secretase
    • Zuo, Z.; Luo, X.; Zhu, W.; Shen, J.; Shen, X.; Jiang, H.; Chen, K. Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with β-secretase. Bioorg. Med. Chem., 2005, 13, 2121-2131.
    • (2005) Bioorg. Med. Chem , vol.13 , pp. 2121-2131
    • Zuo, Z.1    Luo, X.2    Zhu, W.3    Shen, J.4    Shen, X.5    Jiang, H.6    Chen, K.7
  • 177
    • 33644750237 scopus 로고    scopus 로고
    • 3D-QSAR and docking studies of aldehyde inhibitors of human cathepsin K
    • Pan, X.; Tan, N.; Zeng, G.; Huang, H. 3D-QSAR and docking studies of aldehyde inhibitors of human cathepsin K. Bioorg. Med. Chem., 2006, 14, 2771-2778.
    • (2006) Bioorg. Med. Chem , vol.14 , pp. 2771-2778
    • Pan, X.1    Tan, N.2    Zeng, G.3    Huang, H.4
  • 178
    • 33746924874 scopus 로고    scopus 로고
    • Exploration of a binding mode of benzothiazol-2-yl acetonitrile pyrimidine core based derivatives as potent c-Jun N-terminal kinase-3 inhibitors and 3D-QSAR analyses
    • Sharma, P.; Ghoshal, N. Exploration of a binding mode of benzothiazol-2-yl acetonitrile pyrimidine core based derivatives as potent c-Jun N-terminal kinase-3 inhibitors and 3D-QSAR analyses. J. Chem. Inf. Model., 2006, 46, 1763-1774.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1763-1774
    • Sharma, P.1    Ghoshal, N.2
  • 179
    • 33846872804 scopus 로고    scopus 로고
    • Interpretation of scoring functions using 3D molecular fields. mapping the diacylhydrazine-binding pocket of an insect ecdysone receptor
    • Bordas, B.; Belai, I.; Lopata, A.; Szanto, Z. Interpretation of scoring functions using 3D molecular fields. mapping the diacylhydrazine-binding pocket of an insect ecdysone receptor. J. Chem. Inf. Model., 2007, 47, 176-185.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 176-185
    • Bordas, B.1    Belai, I.2    Lopata, A.3    Szanto, Z.4
  • 180
    • 35248826518 scopus 로고    scopus 로고
    • Design of inhibitors of the MurF enzyme of Streptococcus pneumoniae using docking, 3DQSAR, and de Novo design
    • Khedkar, S.A.; Malde, A.K.; Coutinho, E.C. Design of inhibitors of the MurF enzyme of Streptococcus pneumoniae using docking, 3DQSAR, and de Novo design. J. Chem. Inf. Model., 2007, 47, 1839-1846.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1839-1846
    • Khedkar, S.A.1    Malde, A.K.2    Coutinho, E.C.3
  • 181
    • 56849085011 scopus 로고    scopus 로고
    • An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation - A case study with CDK2/CyclinA
    • doi:10.1016/ j.ejmech.2007.10.016
    • Mascarenhas, N.M.; Ghoshal, N. An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation - A case study with CDK2/CyclinA. Eur. J. Med. Chem., 2007, - doi:10.1016/ j.ejmech.2007.10.016.
    • (2007) Eur. J. Med. Chem
    • Mascarenhas, N.M.1    Ghoshal, N.2
  • 182
    • 40049109337 scopus 로고    scopus 로고
    • 3D-QSAR and docking studies of aminopyridine carboxamide inhibitors of c-Jun N-terminal kinase-1
    • Yi, P.; Qiu, M. 3D-QSAR and docking studies of aminopyridine carboxamide inhibitors of c-Jun N-terminal kinase-1. Eur. J. Med. Chem., 2008, 43, 604-613.
    • (2008) Eur. J. Med. Chem , vol.43 , pp. 604-613
    • Yi, P.1    Qiu, M.2
  • 183
    • 45749088639 scopus 로고    scopus 로고
    • Zaheer-ul-Haq; Uddin, R.; Yuan, H.; Pavel A.; Petukhov, P.A.; Choudhary, M. I.; Madura, J.D. Receptor-based modeling and 3DQSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J. Chem. Inf. Model., 2008, 48, 1092-1103.
    • Zaheer-ul-Haq; Uddin, R.; Yuan, H.; Pavel A.; Petukhov, P.A.; Choudhary, M. I.; Madura, J.D. Receptor-based modeling and 3DQSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J. Chem. Inf. Model., 2008, 48, 1092-1103.
  • 184
    • 41149096934 scopus 로고    scopus 로고
    • Structural features of diverse ligands influencing binding affinities to estrogen and estrogen β receptors. Part II. Molecular descriptors calculated from conformation of the ligands in the complex resulting from previous docking study
    • Spreafico, M.; Boriani, E.; Benfenati, E.; Novic, M. Structural features of diverse ligands influencing binding affinities to estrogen and estrogen β receptors. Part II. Molecular descriptors calculated from conformation of the ligands in the complex resulting from previous docking study. Mol. Divers., 2007, 11, 171-181.
    • (2007) Mol. Divers , vol.11 , pp. 171-181
    • Spreafico, M.1    Boriani, E.2    Benfenati, E.3    Novic, M.4
  • 188
    • 44449170479 scopus 로고    scopus 로고
    • Sullivan, D.C; Martin, E.J. ChemInform abstract: Rxploiting structure -
    • Sullivan, D.C; Martin, E.J. ChemInform abstract: Rxploiting structure - activity relationships in docking. J. Chem. Inf. Model., 2008, 48, 817-830.
  • 189
    • 0029000922 scopus 로고
    • Prediction of drug binding affinities by comparative binding energy analysis
    • Ortiz, A.R.; Pisabarro, M.T.; Gago, F.; Wade, R.C. Prediction of drug binding affinities by comparative binding energy analysis. J. Med. Chem., 1995, 38, 2681-2691.
    • (1995) J. Med. Chem , vol.38 , pp. 2681-2691
    • Ortiz, A.R.1    Pisabarro, M.T.2    Gago, F.3    Wade, R.C.4
  • 190
    • 0035866695 scopus 로고    scopus 로고
    • Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes
    • Wang, T.; Wade, R.C. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. J. Med. Chem., 2001, 44, 961-971.
    • (2001) J. Med. Chem , vol.44 , pp. 961-971
    • Wang, T.1    Wade, R.C.2
  • 191
    • 0842304437 scopus 로고    scopus 로고
    • Virtual screening with flexible docking and COMBINE-based models. application to a series of factor Xa inhibitors
    • Murcia, M.; Ortiz, A.R. Virtual screening with flexible docking and COMBINE-based models. application to a series of factor Xa inhibitors. J. Med. Chem., 2004, 47, 805-820.
    • (2004) J. Med. Chem , vol.47 , pp. 805-820
    • Murcia, M.1    Ortiz, A.R.2
  • 192
    • 26944499806 scopus 로고    scopus 로고
    • Antes, I.; Merkwirth, C.; Lengauer, T. POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions. J. Chem. Inf. Model., 2005, 45, 1291-1302.
    • Antes, I.; Merkwirth, C.; Lengauer, T. POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions. J. Chem. Inf. Model., 2005, 45, 1291-1302.
  • 193
    • 0031138166 scopus 로고    scopus 로고
    • The deceptor-like neural network for modeling corticosteroid and testosterone binding globulins
    • Polański, J. The deceptor-like neural network for modeling corticosteroid and testosterone binding globulins. J. Chem. Inf. Comput. Sci., 1997, 37, 553-561.
    • (1997) J. Chem. Inf. Comput. Sci , vol.37 , pp. 553-561
    • Polański, J.1
  • 194
    • 33845772311 scopus 로고    scopus 로고
    • Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
    • Bazeley, P.S.; Prithivi, S.; Struble, C.A.; Povinelli, R.J.; Sem, D.S. Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling. J. Chem. Inf. Model., 2006, 46, 2698-2708.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2698-2708
    • Bazeley, P.S.1    Prithivi, S.2    Struble, C.A.3    Povinelli, R.J.4    Sem, D.S.5
  • 195
    • 34047129815 scopus 로고    scopus 로고
    • A new protein-protein docking scoring function based on interface residue properties
    • Bernauer, J.; Aze', J.; Janin, J.; Poupon, A. A new protein-protein docking scoring function based on interface residue properties. Bionformatics, 2007, 23, 555-562.
    • (2007) Bionformatics , vol.23 , pp. 555-562
    • Bernauer, J.1    Aze', J.2    Janin, J.3    Poupon, A.4
  • 196
    • 1842535990 scopus 로고    scopus 로고
    • Classification Analysis of P-glycoprotein substrate specificity
    • Didziapetris, R.; Japertas, P.; Avdeef, A.; Petrauskas, A. Classification Analysis of P-glycoprotein substrate specificity. J. Drug Target., 2003, 11, 391-406.
    • (2003) J. Drug Target , vol.11 , pp. 391-406
    • Didziapetris, R.1    Japertas, P.2    Avdeef, A.3    Petrauskas, A.4
  • 197
    • 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
  • 198
    • 40949126936 scopus 로고    scopus 로고
    • A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease
    • Fabry-Asztalos, L.; Andonie, R.; Collar, C.J.; Abdul-Wahid, S.; Salim, N. A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease. Bioorg. Med. Chem., 2008, 16, 2903-2911.
    • (2008) Bioorg. Med. Chem , vol.16 , pp. 2903-2911
    • Fabry-Asztalos, L.1    Andonie, R.2    Collar, C.J.3    Abdul-Wahid, S.4    Salim, N.5
  • 199
    • 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
  • 200
    • 26444468103 scopus 로고    scopus 로고
    • Mooij, W.T.M; Verdonk, M.L. General and targeted statistical potentials for protein-ligand interactions. Proteins: Struct. Func. Bioinf., 2005, 61, 272-287.
    • Mooij, W.T.M; Verdonk, M.L. General and targeted statistical potentials for protein-ligand interactions. Proteins: Struct. Func. Bioinf., 2005, 61, 272-287.


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