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Volumn , Issue , 2011, Pages 20-46

Structure-based virtual screening

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EID: 84876841638     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.2174/978160805142711101010020     Document Type: Chapter
Times cited : (4)

References (225)
  • 1
    • 0037362041 scopus 로고    scopus 로고
    • Cheminformatics analysis of organic substituents: Identification of the most common substituents, calculation of substituent properties, and automatic identification of drug-like bioisosteric groups
    • Ertl, P. Cheminformatics analysis of organic substituents: Identification of the most common substituents, calculation of substituent properties, and automatic identification of drug-like bioisosteric groups. J. Chem. Inf. Comput. Sci. 2003, 43, 374-380.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 374-380
    • Ertl, P.1
  • 2
    • 33746058237 scopus 로고    scopus 로고
    • Streamlining lead discovery by aligning in silico and high-throughput screening
    • Davies, J.W.; Glick, M.; Jenkins, J.L. Streamlining lead discovery by aligning in silico and high-throughput screening. Curr. Opin. Chem. Biol. 2006 10, 343-351.
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 343-351
    • Davies, J.W.1    Glick, M.2    Jenkins, J.L.3
  • 3
    • 0037107887 scopus 로고    scopus 로고
    • Structure-based virtual screening: An overview
    • Lyne, P.D. Structure-based virtual screening: An overview. Drug Discov. Today 2002, 7, 1047-1055.
    • (2002) Drug Discov. Today , vol.7 , pp. 1047-1055
    • Lyne, P.D.1
  • 4
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • Shoichet, B.K. Virtual screening of chemical libraries. Nature 2004, 432, 862-865.
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 5
    • 0043069489 scopus 로고    scopus 로고
    • Drug research: Myths, hype and reality
    • Kubinyi, H. Drug research: Myths, hype and reality. Nat. Rev. Drug Discov. 2003, 2, 665-668.
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 665-668
    • Kubinyi, H.1
  • 6
    • 21444438012 scopus 로고    scopus 로고
    • The devil is still in the details-driving early drug discovery forward with biophysical experimental methods
    • Lundqvist, T. The devil is still in the details-driving early drug discovery forward with biophysical experimental methods. Curr. Opin. Drug Discov. Devel. 2005, 8, 513-519.
    • (2005) Curr. Opin. Drug Discov. Devel. , vol.8 , pp. 513-519
    • Lundqvist, T.1
  • 7
    • 3242884966 scopus 로고    scopus 로고
    • High-throughput docking as a source of novel drug leads
    • Alvarez, J.C. High-throughput docking as a source of novel drug leads. Curr. Opin. Chem. Biol. 2004, 8, 365-370.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 365-370
    • Alvarez, J.C.1
  • 8
    • 34548319111 scopus 로고    scopus 로고
    • In silico pharmacology for drug discovery: Applications to targets and beyond
    • Ekins, S.; Mestres, J.; Testa, B. In silico pharmacology for drug discovery: Applications to targets and beyond. Br. J. Pharmacol. 2007, 152, 21-37.
    • (2007) Br. J. Pharmacol. , vol.152 , pp. 21-37
    • Ekins, S.1    Mestres, J.2    Testa, B.3
  • 9
    • 48749127628 scopus 로고    scopus 로고
    • What has virtual screening ever done for drug discovery?
    • Clark, D. What has virtual screening ever done for drug discovery? Expert Opin. Drug Discov. 2008, 3, 841-851.
    • (2008) Expert Opin. Drug Discov. , vol.3 , pp. 841-851
    • Clark, D.1
  • 10
    • 41049113277 scopus 로고    scopus 로고
    • Hierarchical structure-based virtual screening for drug design Biotechnol
    • Miteva, M. Hierarchical structure-based virtual screening for drug design Biotechnol. Biotechnol. Eq. 2008, 22, 634-638.
    • (2008) Biotechnol. Eq. , vol.22 , pp. 634-638
    • Miteva, M.1
  • 11
    • 85056052381 scopus 로고    scopus 로고
    • Screening outside the catalytic site: Inhibition of macromolecular interactions through structure-based virtual ligand screening experiments
    • Sperandio, O.; Miteva, M.A.; Segers, K.; Nicolaes, G.; Villoutreix, B.O. Screening outside the catalytic site: Inhibition of macromolecular interactions through structure-based virtual ligand screening experiments. The Open Biochemistry Journal 2008, 2, 29-37.
    • (2008) The Open Biochemistry Journal , vol.2 , pp. 29-37
    • Sperandio, O.1    Miteva, M.A.2    Segers, K.3    Nicolaes, G.4    Villoutreix, B.O.5
  • 14
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I.D. Structure-based strategies for drug design and discovery. Science 1992, 257, 1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 15
    • 34250332663 scopus 로고    scopus 로고
    • Computer-aided drug design: Integration of structure-based and ligand-based approaches in drug design
    • Prathipati, P.; Dixit, A.; Saxena, A.K. Computer-aided drug design: Integration of structure-based and ligand-based approaches in drug design. Curr. Comp. Aided Drug Design 2007, 3, 341-352.
    • (2007) Curr. Comp. Aided Drug Design , vol.3 , pp. 341-352
    • Prathipati, P.1    Dixit, A.2    Saxena, A.K.3
  • 16
    • 45749109114 scopus 로고    scopus 로고
    • Homology model-based virtual screening for gpcr ligands using docking and targetbiased scoring
    • Radestock, S.; Weil, T.; Renner, S. Homology model-based virtual screening for gpcr ligands using docking and targetbiased scoring. J. Chem. Inf. Model. 2008, 48, 1104-1117.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1104-1117
    • Radestock, S.1    Weil, T.2    Renner, S.3
  • 17
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • Bajorath, J. Integration of virtual and high-throughput screening. Nat. Rev. Drug Discov. 2002, 1, 882-894.
    • (2002) Nat. Rev. Drug Discov. , vol.1 , pp. 882-894
    • Bajorath, J.1
  • 19
    • 15544365691 scopus 로고    scopus 로고
    • New methodologies for ligand-based virtual screening
    • Stahura, F.L.; Bajorath, J. New methodologies for ligand-based virtual screening. Curr. Pharm. De.s 2005, 11, 1189-1202.
    • (2005) Curr. Pharm. De.s , vol.11 , pp. 1189-1202
    • Stahura, F.L.1    Bajorath, J.2
  • 20
    • 84934439821 scopus 로고    scopus 로고
    • Molecular similarity concepts and search calculations
    • Auer, J.; Bajorath, J. Molecular similarity concepts and search calculations. Methods Mol. Biol. 2008, 453, 327-347.
    • (2008) Methods Mol. Biol. , vol.453 , pp. 327-347
    • Auer, J.1    Bajorath, J.2
  • 21
    • 54749090921 scopus 로고    scopus 로고
    • Ligand-based approaches in virtual screening
    • Douguet, D. Ligand-based approaches in virtual screening. Curr. Comp. Aided Drug Design 2008, 4, 180-190.
    • (2008) Curr. Comp. Aided Drug Design , vol.4 , pp. 180-190
    • Douguet, D.1
  • 23
    • 0347755444 scopus 로고    scopus 로고
    • Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking
    • Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H.J. Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr. Med. Chem. 2004, 11, 91-107.
    • (2004) Curr. Med. Chem. , vol.11 , pp. 91-107
    • Schneidman-duhovny, D.1    Nussinov, R.2    Wolfson, H.J.3
  • 24
    • 33749513381 scopus 로고    scopus 로고
    • Receptor-based computational screening of compound databases: The main docking-scoring engines
    • Sperandio, O.; Miteva, M.A.; Delfaud, F.; Villoutreix, B.O. Receptor-based computational screening of compound databases: The main docking-scoring engines. Curr. Protein Pept. Sci. 2006, 7, 369-393.
    • (2006) Curr. Protein Pept. Sci. , vol.7 , pp. 369-393
    • Sperandio, O.1    Miteva, M.A.2    Delfaud, F.3    Villoutreix, B.O.4
  • 25
    • 34547661861 scopus 로고    scopus 로고
    • Comparative performance of several flexible docking programs and scoring functions: Enrichment studies 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: Enrichment studies 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
  • 26
    • 0036720460 scopus 로고    scopus 로고
    • Progress toward virtual screening for drug side effects
    • Rockey, W.M.; Elcock, A.H. Progress toward virtual screening for drug side effects. Proteins 2002, 48, 664-671.
    • (2002) Proteins , vol.48 , pp. 664-671
    • Rockey, W.M.1    Elcock, A.H.2
  • 27
    • 6044260116 scopus 로고    scopus 로고
    • Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model
    • Evers, A.; Klebe, G. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model. J. Med. Chem. 2004, 47, 5381-5392.
    • (2004) J. Med. Chem. , vol.47 , pp. 5381-5392
    • Evers, A.1    Klebe, G.2
  • 28
    • 33244475355 scopus 로고    scopus 로고
    • Screening drug-like compounds by docking to homology models: A systematic study
    • Kairys, V.; Fernandes, M.X.; Gilson, M.K. Screening drug-like compounds by docking to homology models: A systematic study. J. Chem. Inf. Model. 2006, 46, 365-379.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 365-379
    • Kairys, V.1    Fernandes, M.X.2    Gilson, M.K.3
  • 30
    • 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 Discov. 2004, 3, 935-949.
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 31
    • 34447275949 scopus 로고    scopus 로고
    • Ligand docking and structure-based virtual screening in drug discovery
    • Cavasotto, C.N.; Orry, A.J. Ligand docking and structure-based virtual screening in drug discovery. Curr. Top. Med. Chem. 2007, 7, 1015-1023.
    • (2007) Curr. Top. Med. Chem. , vol.7 , pp. 1015-1023
    • Cavasotto, C.N.1    Orry, A.J.2
  • 33
    • 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
  • 36
    • 34548200847 scopus 로고    scopus 로고
    • Structure-based drug design: Docking and scoring
    • Kroemer, R.T. Structure-based drug design: Docking and scoring Curr. Prot. Peptide Sci. 2007, 8, 312-328.
    • (2007) Curr. Prot. Peptide Sci. , vol.8 , pp. 312-328
    • Kroemer, R.T.1
  • 37
    • 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.; 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, S7-26.
    • Br. J. Pharmacol.
    • Moitessier, N.1    Englebienne, P.2    Lee, D.3    Lawandi, J.4    Corbeil, C.R.5
  • 38
    • 84884434964 scopus 로고    scopus 로고
    • Virtual ligand screening for structure-based drug design: Approaches and progress
    • Miteva, M.A.; Sperandio, O.; Villoutreix, B.O. Virtual ligand screening for structure-based drug design: Approaches and progress. Bioautomation 2007, 7, 104-121.
    • (2007) Bioautomation , vol.7 , pp. 104-121
    • Miteva, M.A.1    Sperandio, O.2    Villoutreix, B.O.3
  • 40
    • 33747200808 scopus 로고    scopus 로고
    • Combining docking and molecular dynamic simulations in drug design
    • Alonso, H.; Bliznyuk, A.A.; Gready, J.E. Combining docking and molecular dynamic simulations in drug design. Med. Res. Rev. 2006, 26, 531-568.
    • (2006) Med. Res. Rev. , vol.26 , pp. 531-568
    • Alonso, H.1    Bliznyuk, A.A.2    Gready, J.E.3
  • 42
    • 64049102289 scopus 로고    scopus 로고
    • Binding of small-molecule ligands to proteins: "What you see" Is not always "What you get"
    • Mobley, D.L.; Dill, K.A. Binding of small-molecule ligands to proteins: "What you see" Is not always "What you get". Structure 2009, 17, 489-498.
    • (2009) Structure , vol.17 , pp. 489-498
    • Mobley, D.L.1    Dill, K.A.2
  • 43
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist, J.; Medina, C.; Samuelsson, J.E. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 1994, 7, 385-391.
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 44
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • Jain, A.N. Scoring functions for protein-ligand docking. Curr. Protein Pept. Sci 2006, 7, 407-420.
    • (2006) Curr. Protein Pept. Sci , vol.7 , pp. 407-420
    • Jain, A.N.1
  • 45
    • 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
  • 46
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell, D.S.; Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 1990, 8, 195-202.
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 47
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • Shoichet, B.K.; Leach, A.R.; Kuntz, I.D. Ligand solvation in molecular docking. Proteins 1999, 34, 4-16.
    • (1999) Proteins , vol.34 , pp. 4-16
    • Shoichet, B.K.1    Leach, A.R.2    Kuntz, I.D.3
  • 48
    • 0033536456 scopus 로고    scopus 로고
    • Inclusion of solvation in ligand binding free energy calculations using the generalized-born model
    • Zou, X.; Sun, Y.; Kuntz, I.D. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model J. Am. Chem. Soc. 1999, 121, 8033-8043.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 8033-8043
    • Zou, X.1    Sun, Y.2    Kuntz, I.D.3
  • 49
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • Wang, J.; Morin, P.; Wang, W.; Kollman, P.A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 2001, 123, 5221-5230.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 50
    • 1542741046 scopus 로고    scopus 로고
    • Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring
    • Yoon, S.; Welsh, W.J. Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring J. Chem. Inf. Comput. Sci. 2004, 44, 88-96.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 88-96
    • Yoon, S.1    Welsh, W.J.2
  • 51
    • 33746872935 scopus 로고    scopus 로고
    • Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring
    • Lyne, P.D.; Lamb, M.L.; Saeh, J.C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J. Med. Chem. 2006, 49, 4805-4808.
    • (2006) J. Med. Chem. , vol.49 , pp. 4805-4808
    • Lyne, P.D.1    Lamb, M.L.2    Saeh, J.C.3
  • 52
    • 35348864558 scopus 로고    scopus 로고
    • Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors
    • Ferrari, A.M.; Degliesposti, G.; Sgobba, M.; Rastelli, G. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. Bioorg. Med. Chem. 2007, 15, 7865-7877.
    • (2007) Bioorg. Med. Chem. , vol.15 , pp. 7865-7877
    • Ferrari, A.M.1    Degliesposti, G.2    Sgobba, M.3    Rastelli, G.4
  • 54
    • 17144414125 scopus 로고    scopus 로고
    • Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
    • Wang, J.; Kang, X.; Kuntz, I.D.; Kollman, P.A. Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J. Med. Chem. 2005, 48, 2432-2444.
    • (2005) J. Med. Chem. , vol.48 , pp. 2432-2444
    • Wang, J.1    Kang, X.2    Kuntz, I.D.3    Kollman, P.A.4
  • 55
    • 33845493850 scopus 로고    scopus 로고
    • Protein-ligand binding affinity predictions by implicit solvent simulations: A tool for lead optimization?
    • Michel, J.; Verdonk, M.L.; Essex, J.W. Protein-ligand binding affinity predictions by implicit solvent simulations: A tool for lead optimization? J. Med. Chem. 2006, 49, 7427-7439.
    • (2006) J. Med. Chem. , vol.49 , pp. 7427-7439
    • Michel, J.1    Verdonk, M.L.2    Essex, J.W.3
  • 56
    • 33645400172 scopus 로고    scopus 로고
    • A multistep approach to structure-based drug design: Studying ligand binding at the human neutrophil elastase
    • Steinbrecher, T.; Case, D.A.; Labahn, A. A multistep approach to structure-based drug design: Studying ligand binding at the human neutrophil elastase. J. Med. Chem. 2006, 49, 1837-1844.
    • (2006) J. Med. Chem. , vol.49 , pp. 1837-1844
    • Steinbrecher, T.1    Case, D.A.2    Labahn, A.3
  • 58
    • 56449121765 scopus 로고    scopus 로고
    • Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity
    • Kulharia, M.; Goody, R.S.; Jackson, R.M. Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity. J. Chem. Inf. Model. 2008, 48, 1990-1998.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1990-1998
    • Kulharia, M.1    Goody, R.S.2    Jackson, R.M.3
  • 59
    • 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 structure
    • Bohm, H.J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 1994, 8, 243-256.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 60
    • 0029933286 scopus 로고    scopus 로고
    • Prediction of protein complexes using empirical free energy functions
    • Weng, Z.; Vajda, S.; Delisi, C. Prediction of protein complexes using empirical free energy functions. Protein Sci. 1996, 5, 614-626.
    • (1996) Protein Sci. , vol.5 , pp. 614-626
    • Weng, Z.1    Vajda, S.2    Delisi, C.3
  • 61
    • 13444292556 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand interactions: A critical perspective
    • Schulz-Gasch, T.; Stah, M. Scoring functions for protein-ligand interactions: A critical perspective. Drug Discovery Today: Technologies 2004, 1, 231-239.
    • (2004) Drug Discovery Today: Technologies , vol.1 , pp. 231-239
    • Schulz-gasch, T.1    Stah, M.2
  • 62
    • 53249117061 scopus 로고    scopus 로고
    • Evaluation of ligand-binding affinity using polynomial empirical scoring functions
    • de Azevedo, W.F., Jr.; Dias, R. Evaluation of ligand-binding affinity using polynomial empirical scoring functions. Bioorg. Med. Chem. 2008, 16, 9378-9382.
    • (2008) Bioorg. Med. Chem. , vol.16 , pp. 9378-9382
    • De Azevedo Jr, W.F.1    Dias, R.2
  • 63
    • 49449105293 scopus 로고    scopus 로고
    • AIscore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes
    • Raub, S.; Steffen, A.; Kamper, A.; Marian, C.M. AIscore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes. J. Chem. Inf. Model. 2008, 48, 1492-1510.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1492-1510
    • Raub, S.1    Steffen, A.2    Kamper, A.3    Marian, C.M.4
  • 64
    • 35348868045 scopus 로고    scopus 로고
    • A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations
    • Wang, B.; Westerhoff, L.M.; Merz, K.M., Jr. A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J. Med. Chem. 2007, 50, 5128-5134.
    • (2007) J. Med. Chem. , vol.50 , pp. 5128-5134
    • Wang, B.1    Westerhoff, L.M.2    Merz Jr, K.M.3
  • 65
    • 0029119320 scopus 로고
    • A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
    • Wallqvist, A.; Jernigan, R.L.; Covell, D.G. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci. 1995, 4, 1881-1903.
    • (1995) Protein Sci. , vol.4 , pp. 1881-1903
    • Wallqvist, A.1    Jernigan, R.L.2    Covell, D.G.3
  • 66
    • 33750574927 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: Ii. Validation of the scoring function
    • Huang, S.Y.; Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: Ii. Validation of the scoring function. J. Comput. Chem. 2006, 27, 1876-1882.
    • (2006) J. Comput. Chem. , vol.27 , pp. 1876-1882
    • Huang, S.Y.1    Zou, X.2
  • 67
    • 4143082530 scopus 로고    scopus 로고
    • Native atom types for knowledge-based potentials: Application to binding energy prediction
    • Dominy, B.N.; Shakhnovich, E.I. Native atom types for knowledge-based potentials: Application to binding energy prediction. J. Med. Chem. 2004, 47, 4538-4558.
    • (2004) J. Med. Chem. , vol.47 , pp. 4538-4558
    • Dominy, B.N.1    Shakhnovich, E.I.2
  • 68
    • 34247263219 scopus 로고    scopus 로고
    • A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins(FLAP): Theory and application
    • Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J.S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins(FLAP): Theory and application. J. Chem. Inf. Model. 2007, 47, 279-294.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 279-294
    • Baroni, M.1    Cruciani, G.2    Sciabola, S.3    Perruccio, F.4    Mason, J.S.5
  • 69
    • 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
  • 70
    • 67349104587 scopus 로고    scopus 로고
    • Targeted scoring functions for virtual screening
    • Seifert, M.H. Targeted scoring functions for virtual screening. Drug Discov. Today 2009, 14, 562-569.
    • (2009) Drug Discov. Today , vol.14 , pp. 562-569
    • Seifert, M.H.1
  • 71
    • 42149183130 scopus 로고    scopus 로고
    • Optimizing the signal-to-noise ratio of scoring functions for protein-ligand docking
    • Seifert, M.H. Optimizing the signal-to-noise ratio of scoring functions for protein-ligand docking. J. Chem. Inf. Model. 2008, 48, 602-612.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 602-612
    • Seifert, M.H.1
  • 74
    • 0346731233 scopus 로고    scopus 로고
    • Multiple active site corrections for docking and virtual screening
    • Vigers, G.P.; Rizzi, J.P. Multiple active site corrections for docking and virtual screening. J. Med. Chem. 2004, 47, 80-89.
    • (2004) J. Med. Chem. , vol.47 , pp. 80-89
    • Vigers, G.P.1    Rizzi, J.P.2
  • 75
    • 0028412035 scopus 로고
    • Flog: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure
    • Miller, M.D.; Kearsley, S.K.; Underwood, D.J.; Sheridan, R.P. Flog: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure. J. Comput. Aided Mol. Des. 1994, 8, 153-174.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 153-174
    • Miller, M.D.1    Kearsley, S.K.2    Underwood, D.J.3    Sheridan, R.P.4
  • 76
    • 0026570977 scopus 로고
    • Clix: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure
    • Lawrence, M.C.; Davis, P.C. Clix: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure. Proteins 1992, 12, 31-41.
    • (1992) Proteins , vol.12 , pp. 31-41
    • Lawrence, M.C.1    Davis, P.C.2
  • 77
    • 0035976367 scopus 로고    scopus 로고
    • Eudoc: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
    • Pang, Y.P.; Perola, E.; Xu, K.; Prendergast, F.G. Eudoc: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J. Comput. Chem. 2001, 22, 1750-1771.
    • (2001) J. Comput. Chem. , vol.22 , pp. 1750-1771
    • Pang, Y.P.1    Perola, E.2    Xu, K.3    Prendergast, F.G.4
  • 78
    • 13944253576 scopus 로고    scopus 로고
    • Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors
    • Mozziconacci, J.C.; Arnoult, E.; Bernard, P.; Do, Q.T.; Marot, C.; Morin-Allory, L. Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors. J. Med. Chem. 2005, 48, 1055-1068.
    • (2005) J. Med. Chem. , vol.48 , pp. 1055-1068
    • Mozziconacci, J.C.1    Arnoult, E.2    Bernard, P.3    Do, Q.T.4    Marot, C.5    Morin-allory, L.6
  • 79
    • 24944433024 scopus 로고    scopus 로고
    • Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex
    • Miteva, M.A.; Lee, W.H.; Montes, M.O.; Villoutreix, B.O. Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex. J. Med. Chem. 2005, 48, 6012-6022.
    • (2005) J. Med. Chem. , vol.48 , pp. 6012-6022
    • Miteva, M.A.1    Lee, W.H.2    Montes, M.O.3    Villoutreix, B.O.4
  • 80
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber, D.M.; Shoichet, B.K. Flexible ligand docking using conformational ensembles. Protein Sci. 1998, 7, 938-950.
    • (1998) Protein Sci. , vol.7 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 81
    • 23844444239 scopus 로고    scopus 로고
    • Hierarchical docking of databases of multiple ligand conformations
    • Lorber, D.M.; Shoichet, B.K. Hierarchical docking of databases of multiple ligand conformations. Curr. Top. Med. Chem. 2005, 5, 739-749.
    • (2005) Curr. Top. Med. Chem. , vol.5 , pp. 739-749
    • Lorber, D.M.1    Shoichet, B.K.2
  • 82
    • 43049146552 scopus 로고    scopus 로고
    • MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
    • Sauton, N.; Lagorce, D.; Villoutreix, B.O.; Miteva, M.A. MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics 2008, 9, 184.
    • (2008) BMC Bioinformatics , vol.9 , pp. 184
    • Sauton, N.1    Lagorce, D.2    Villoutreix, B.O.3    Miteva, M.A.4
  • 84
    • 33746921247 scopus 로고    scopus 로고
    • Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations
    • Kirchmair, J.; Wolber, G.; Laggner, C.; Langer, T. Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations. J. Chem. Inf. Model. 2006, 46, 1848-1861.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1848-1861
    • Kirchmair, J.1    Wolber, G.2    Laggner, C.3    Langer, T.4
  • 85
    • 61349109390 scopus 로고    scopus 로고
    • MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space
    • Sperandio, O.; Souaille, M.; Delfaud, F.; Miteva, M.A.; Villoutreix, B.O. MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Eur. J. Med. Chem. 2009, 44, 1405-1409.
    • (2009) Eur. J. Med. Chem. , vol.44 , pp. 1405-1409
    • Sperandio, O.1    Souaille, M.2    Delfaud, F.3    Miteva, M.A.4    Villoutreix, B.O.5
  • 87
    • 37249065124 scopus 로고    scopus 로고
    • Generating conformer ensembles using a multiobjective genetic algorithm
    • Vainio, M.J.; Johnson, M.S. Generating conformer ensembles using a multiobjective genetic algorithm. J. Chem. Inf. Model. 2007, 47, 2462-2474.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 2462-2474
    • Vainio, M.J.1    Johnson, M.S.2
  • 88
    • 72749127604 scopus 로고    scopus 로고
    • DG-AMMOS: A new tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening
    • Lagorce, D.; Pencheva, T.; Villoutreix, B.O.; Miteva, M.A. DG-AMMOS: A new tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening. BMC Chem. Biol. 2009, 9, 6.
    • (2009) BMC Chem. Biol. , vol.9 , pp. 6
    • Lagorce, D.1    Pencheva, T.2    Villoutreix, B.O.3    Miteva, M.A.4
  • 89
    • 0001139413 scopus 로고    scopus 로고
    • Automated flexible ligand docking method and its application for database search J
    • Makino, S.; Kuntz, I.D. Automated flexible ligand docking method and its application for database search J. Comput. Chem. 1997, 18, 1812-1825.
    • (1997) Comput. Chem. , vol.18 , pp. 1812-1825
    • Makino, S.1    Kuntz, I.D.2
  • 90
    • 0035971738 scopus 로고    scopus 로고
    • A smooth permittivity function for Poisson-Boltzmann solvation methods
    • Grant, J.A.; Pickup, B.T.; Nicholls, A. A smooth permittivity function for Poisson-Boltzmann solvation methods. J. Comp. Chem. 2001, 22, 608-640.
    • (2001) J. Comp. Chem. , vol.22 , pp. 608-640
    • Grant, J.A.1    Pickup, B.T.2    Nicholls, A.3
  • 91
    • 0034284367 scopus 로고    scopus 로고
    • Similarity-driven flexible ligand docking
    • Fradera, X.; Knegtel, R.M.; Mestres, J. Similarity-driven flexible ligand docking. Proteins 2000, 40, 623-636.
    • (2000) Proteins , vol.40 , pp. 623-636
    • Fradera, X.1    Knegtel, R.M.2    Mestres, J.3
  • 93
    • 0037434582 scopus 로고    scopus 로고
    • Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
    • Jain, A.N. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem. 2003, 46, 499-511.
    • (2003) J. Med. Chem. , vol.46 , pp. 499-511
    • Jain, A.N.1
  • 94
    • 34247343346 scopus 로고    scopus 로고
    • Surflex-dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
    • Jain, A.N. Surflex-dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J. Comput. Aided Mol. Des. 2007, 21, 281-306.
    • (2007) J. Comput. Aided Mol. Des. , vol.21 , pp. 281-306
    • Jain, A.N.1
  • 95
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch, W.; Ruppert, J.; Jain, A.N. Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 1996, 3, 449-462.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 96
    • 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
  • 97
    • 0026813925 scopus 로고
    • The computer program ludi: A new method for the de novo design of enzyme inhibitors
    • Bohm, 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
    • Bohm, H.J.1
  • 98
    • 0028522365 scopus 로고
    • A fast and efficient method to generate biologically relevant conformations
    • Klebe, G.; Mietzner, T. A fast and efficient method to generate biologically relevant conformations. J. Comput. Aided Mol. Des. 1994, 8, 583-606.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 583-606
    • Klebe, G.1    Mietzner, T.2
  • 100
    • 0037212102 scopus 로고    scopus 로고
    • Ligandfit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam, C.M.; Jiang, X.; Oldfield, T.; Waldman, M. Ligandfit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model. 2003, 21, 289-307.
    • (2003) J. Mol. Graph. Model. , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 103
    • 0032855301 scopus 로고    scopus 로고
    • Mcdock: A Monte Carlo simulation approach to the molecular docking problem
    • Liu, M.; Wang, S. Mcdock: A Monte Carlo simulation approach to the molecular docking problem. J. Comput. Aided Mol. Des. 1999, 13, 435-451.
    • (1999) J. Comput. Aided Mol. Des. , vol.13 , pp. 435-451
    • Liu, M.1    Wang, S.2
  • 104
    • 0031297617 scopus 로고    scopus 로고
    • Critical evaluation of the research docking program for the CASP2 challenge
    • Hart, T.N.; Ness, S.R.; Read, R.J. Critical evaluation of the research docking program for the CASP2 challenge. Proteins 1997, Suppl 1, 205-209.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 205-209
    • Hart, T.N.1    Ness, S.R.2    Read, R.J.3
  • 105
    • 0031181346 scopus 로고    scopus 로고
    • Qxp: 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.2
  • 106
    • 34250801603 scopus 로고    scopus 로고
    • QUASI: A novel method for simultaneous superposition of multiple flexible ligands and virtual screening using partial similarity
    • Todorov, N.P.; Alberts, I.L.; Esch, I.J.; Dean, P.M. QUASI: A novel method for simultaneous superposition of multiple flexible ligands and virtual screening using partial similarity. J. Chem. Inf. Model. 2007, 47, 1007-1020.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1007-1020
    • Todorov, N.P.1    Alberts, I.L.2    Esch, I.J.3    Dean, P.M.4
  • 107
    • 34547702155 scopus 로고    scopus 로고
    • GlamDock: Development and validation of a new docking tool on several thousand proteinligand complexes
    • Tietze, S.; Apostolakis, J. GlamDock: Development and validation of a new docking tool on several thousand proteinligand complexes. J. Chem. Inf. Model. 2007, 47, 1657-1672.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1657-1672
    • Tietze, S.1    Apostolakis, J.2
  • 108
    • 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
  • 109
    • 0034332970 scopus 로고    scopus 로고
    • Darwin: A program for docking flexible molecules
    • Taylor, J.S.; Burnett, R.M. Darwin: A program for docking flexible molecules. Proteins 2000, 41, 173-191.
    • (2000) Proteins , vol.41 , pp. 173-191
    • Taylor, J.S.1    Burnett, R.M.2
  • 110
    • 0742269481 scopus 로고    scopus 로고
    • Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
    • Cecchini, M.; Kolb, P.; Majeux, N.; Caflisch, A. Automated docking of highly flexible ligands by genetic algorithms: A critical assessment J. Comput. Chem. 2004, 25, 412-422.
    • (2004) J. Comput. Chem. , vol.25 , pp. 412-422
    • Cecchini, M.1    Kolb, P.2    Majeux, N.3    Caflisch, A.4
  • 111
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R. K.; Olson, A.J. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1999, 19, 1639-1662.
    • (1999) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 112
    • 33748173818 scopus 로고    scopus 로고
    • BDT: An easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
    • Vaque, M.; Arola, A.; Aliagas, C.; Pujadas, G. BDT: An easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics 2006, 22, 1803-1804.
    • (2006) Bioinformatics , vol.22 , pp. 1803-1804
    • Vaque, M.1    Arola, A.2    Aliagas, C.3    Pujadas, G.4
  • 114
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455-461.
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 115
    • 36348989005 scopus 로고    scopus 로고
    • PSOamp;AUTODOCK: A fast flexible molecular docking program based on swarm intelligence
    • Namasivayam, V.; Günther, R. PSO&AUTODOCK: A fast flexible molecular docking program based on swarm intelligence. Chem. Biol. Drug Des. 2007, 70, 475-484.
    • (2007) Chem. Biol. Drug Des. , vol.70 , pp. 475-484
    • Namasivayam, V.1    Günther, R.2
  • 116
    • 58149133913 scopus 로고    scopus 로고
    • Lead Finder: An approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening
    • Stroganov, O.V.; Novikov, F.N.; Stroylov, V.S.; Kulkov, V.; Chilov, G.G. Lead Finder: An approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening. J. Chem. Inf. Model. 2008, 48, 2371-2385.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2371-2385
    • Stroganov, O.V.1    Novikov, F.N.2    Stroylov, V.S.3    Kulkov, V.4    Chilov, G.G.5
  • 117
    • 0032533791 scopus 로고    scopus 로고
    • Flexible docking using tabu search and an empirical estimate of binding affinity
    • Baxter, C.A.; Murray, C.W.; Clark, D.E.; Westhead, D.R.; Eldridge, M.D. Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 1998, 33, 367-382.
    • (1998) Proteins , vol.33 , pp. 367-382
    • Baxter, C.A.1    Murray, C.W.2    Clark, D.E.3    Westhead, D.R.4    Eldridge, M.D.5
  • 118
    • 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 2006, 62, 934-946.
    • (2006) Proteins , vol.62 , pp. 934-946
    • Pei, J.1    Wang, Q.2    Liu, Z.3    Li, Q.4    Yang, K.5    Lai, L.6
  • 119
    • 42449150833 scopus 로고    scopus 로고
    • High quality binding modes in docking ligands to proteins
    • Gorelik, B.; Goldblum, A. High quality binding modes in docking ligands to proteins. Proteins 2008, 71, 1373-1386.
    • (2008) Proteins , vol.71 , pp. 1373-1386
    • Gorelik, B.1    Goldblum, A.2
  • 120
    • 33751358567 scopus 로고    scopus 로고
    • PLANTS: Application of ant colony optimization to structure-based drug design
    • ANTS LNCS 4150
    • Korb, O.; Stutzle, T.; Exner, T.E. PLANTS: Application of ant colony optimization to structure-based drug design. 2006; ANTS LNCS 4150, pp. 247-258.
    • (2006) , pp. 247-258
    • Korb, O.1    Stutzle, T.2    Exner, T.E.3
  • 121
    • 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
  • 122
    • 25844478436 scopus 로고    scopus 로고
    • In-silico screening using flexible ligand binding pockets: A molecular dynamics-based approach
    • Sivanesan, D.; Rajnarayanan, R.V.; Doherty, J.; Pattabiraman, N. In-silico screening using flexible ligand binding pockets: A molecular dynamics-based approach. J. Comput. Aided Mol. Des. 2005, 19, 213-228.
    • (2005) J. Comput. Aided Mol. Des. , vol.19 , pp. 213-228
    • Sivanesan, D.1    Rajnarayanan, R.V.2    Doherty, J.3    Pattabiraman, N.4
  • 123
    • 65249157200 scopus 로고    scopus 로고
    • In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking
    • Bolstad, E.S.; Anderson, A.C. In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking. Proteins 2009, 75, 62-74.
    • (2009) Proteins , vol.75 , pp. 62-74
    • Bolstad, E.S.1    Anderson, A.C.2
  • 124
    • 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
  • 125
    • 20444377245 scopus 로고    scopus 로고
    • Validation and use of the MM-PBSA approach for drug discovery
    • Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and use of the MM-PBSA approach for drug discovery. J. Med. Chem. 2005, 48, 4040-4048.
    • (2005) J. Med. Chem. , vol.48 , pp. 4040-4048
    • Kuhn, B.1    Gerber, P.2    Schulz-gasch, T.3    Stahl, M.4
  • 126
    • 23944459025 scopus 로고    scopus 로고
    • A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
    • Khandelwal, A.; Lukacova, V.; Comez, D.; Kroll, D.M.; Raha, S.; Balaz, S. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J. Med. Chem. 2005, 48, 5437-5447.
    • (2005) J. Med. Chem. , vol.48 , pp. 5437-5447
    • Khandelwal, A.1    Lukacova, V.2    Comez, D.3    Kroll, D.M.4    Raha, S.5    Balaz, S.6
  • 127
    • 33244496700 scopus 로고    scopus 로고
    • New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2
    • Ferrara, P.; Curioni, A.; Vangrevelinghe, E.; Meyer, T.; Mordasini, T.; Andreoni, W.; Acklin, P.; Jacoby, E. New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2. J. Chem. Inf. Model. 2006, 46, 254-263.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 254-263
    • Ferrara, P.1    Curioni, A.2    Vangrevelinghe, E.3    Meyer, T.4    Mordasini, T.5    Andreoni, W.6    Acklin, P.7    Jacoby, E.8
  • 128
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S.J. Implications of protein flexibility for drug discovery Nat. Rev. Drug Discov. 2003, 2, 527-541.
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 129
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand docking and virtual screening to protein kinases
    • Cavasotto, C.N.; Abagyan, R.A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 2004, 337, 209-225.
    • (2004) J. Mol. Biol. , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 131
    • 33846635484 scopus 로고    scopus 로고
    • Targeting structural flexibility in HIV-1 protease inhibitor binding
    • Hornak, V.; Simmerling, C. Targeting structural flexibility in HIV-1 protease inhibitor binding. Drug Discov. Today 2007, 12, 132-138.
    • (2007) Drug Discov. Today , vol.12 , pp. 132-138
    • Hornak, V.1    Simmerling, C.2
  • 132
    • 0035630691 scopus 로고    scopus 로고
    • Protein-protein interfaces: Mimics and inhibitors
    • Cochran, A.G. Protein-protein interfaces: Mimics and inhibitors. Curr. Opin. Chem. Biol. 2001, 5, 654-659.
    • (2001) Curr. Opin. Chem. Biol. , vol.5 , pp. 654-659
    • Cochran, A.G.1
  • 133
    • 0037061646 scopus 로고    scopus 로고
    • Inhibition of protein-protein association by small molecules: Approaches and progress
    • Toogood, P.L. Inhibition of protein-protein association by small molecules: Approaches and progress. J. Med. Chem. 2002, 45, 1543-1558.
    • (2002) J. Med. Chem. , vol.45 , pp. 1543-1558
    • Toogood, P.L.1
  • 134
    • 21244479779 scopus 로고    scopus 로고
    • Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
    • Barril, X.; Morley, S.D. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J. Med. Chem. 2005, 48, 4432-4443.
    • (2005) J. Med. Chem. , vol.48 , pp. 4432-4443
    • Barril, X.1    Morley, S.D.2
  • 135
    • 33746924045 scopus 로고    scopus 로고
    • Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and betasecretase
    • Polgar, T.; Keseru, G.M. Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and betasecretase. J. Chem. Inf. Model. 2006, 46, 1795-1805.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1795-1805
    • Polgar, T.1    Keseru, G.M.2
  • 136
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr. Opin. Struct. Biol. 2008, 18, 178-184.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 137
    • 0346731234 scopus 로고    scopus 로고
    • HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases
    • Floriano, W.B.; Vaidehi, N.; Zamanakos, G.; Goddard, W.A., 3rd. HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. J. Med. Chem. 2004, 47, 56-71.
    • (2004) J. Med. Chem. , vol.47 , pp. 56-71
    • Floriano, W.B.1    Vaidehi, N.2    Zamanakos, G.3    Goddard, W.A.4
  • 142
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T.A.; Murphy, R.B.; Friesner, R.A.; Beard, H.S.; Frye, L.L.; Pollard, W.T.; Banks, J.L. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47, 1750-1759.
    • (2004) J. Med. Chem. , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5    Pollard, W.T.6    Banks, J.L.7
  • 143
    • 34250829729 scopus 로고    scopus 로고
    • Alternative to consensus scoring-a new approach toward the qualitative combination of docking algorithms
    • Wolf, A.; Zimmermann, M.; Hofmann-Apitius, M. Alternative to consensus scoring-a new approach toward the qualitative combination of docking algorithms. J. Chem. Inf. Model. 2007, 47, 1036-1044.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1036-1044
    • Wolf, A.1    Zimmermann, M.2    Hofmann-apitius, M.3
  • 144
    • 23844487874 scopus 로고    scopus 로고
    • Enhanced virtual screening by combined use of two docking methods: Getting the most on a limited budget
    • Maiorov, V.; Sheridan, R.P. Enhanced virtual screening by combined use of two docking methods: Getting the most on a limited budget. J. Chem. Inf. Model. 2005, 45, 1017-1023.
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 1017-1023
    • Maiorov, V.1    Sheridan, R.P.2
  • 146
    • 53549091061 scopus 로고    scopus 로고
    • Discovery of novel nitrobenzothiazole unhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening
    • Cho, Y.; Ioerger, T.R.; Sacchettini, J.C. Discovery of novel nitrobenzothiazole unhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. J. Med. Chem. 2008, 51, 5984-5992
    • (2008) J. Med. Chem. , vol.51 , pp. 5984-5992
    • Cho, Y.1    Ioerger, T.R.2    Sacchettini, J.C.3
  • 148
    • 27444439094 scopus 로고    scopus 로고
    • Structure-based virtual screening for low molecular weight chemical starting points for dipeptidyl peptidase iv inhibitors
    • Ward, R.A.; Perkins, T.D.; Stafford, J. Structure-based virtual screening for low molecular weight chemical starting points for dipeptidyl peptidase iv inhibitors. J. Med. Chem. 2005, 48, 6991-6996.
    • (2005) J. Med. Chem. , vol.48 , pp. 6991-6996
    • Ward, R.A.1    Perkins, T.D.2    Stafford, J.3
  • 151
    • 34548525877 scopus 로고    scopus 로고
    • Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening
    • Hirayama, K.; Aoki, S.; Nishikawa, K.; Matsumoto, T.; Wada, K. Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening. Bioorg. Med. Chem. 2007, 15, 6810-6818.
    • (2007) Bioorg. Med. Chem. , vol.15 , pp. 6810-6818
    • Hirayama, K.1    Aoki, S.2    Nishikawa, K.3    Matsumoto, T.4    Wada, K.5
  • 152
    • 53549132514 scopus 로고    scopus 로고
    • Pyrazolidine-3,5-dione derivatives as potent non-steroidal agonists of farnesoid X receptor: Virtual screening, synthesis, and biological evaluation
    • Deng, G.; Li, W.; Shen, J.; Jiang, H.; Chen, K.; Liu, H. Pyrazolidine-3,5-dione derivatives as potent non-steroidal agonists of farnesoid X receptor: Virtual screening, synthesis, and biological evaluation. Bioorg. Med. Chem. Lett. 2008, 18, 5497-5502.
    • (2008) Bioorg. Med. Chem. Lett. , vol.18 , pp. 5497-5502
    • Deng, G.1    Li, W.2    Shen, J.3    Jiang, H.4    Chen, K.5    Liu, H.6
  • 153
    • 61949212798 scopus 로고    scopus 로고
    • Knowledge based identification of potent antitubercular compounds using structure based virtual screening and structure interaction fingerprints
    • Kumar, A.; Chaturvedi, V.; Bhatnagar, S.; Sinha, S.; Siddiqi, M. I. Knowledge based identification of potent antitubercular compounds using structure based virtual screening and structure interaction fingerprints. J. Chem. Inf. Model. 2009, 49, 35-42.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 35-42
    • Kumar, A.1    Chaturvedi, V.2    Bhatnagar, S.3    Sinha, S.4    Siddiqi, M.I.5
  • 154
    • 54049118742 scopus 로고    scopus 로고
    • Discovery of substituted sulfonamides and thiazolidin-4-one derivatives as agonists of human constitutive androstane receptor
    • Küblbeck, J.; Jyrkkärinne, J.; Poso, A.; Turpeinen, M.; Sippl, W.; Honkakoski, P.; Windshügel, B. Discovery of substituted sulfonamides and thiazolidin-4-one derivatives as agonists of human constitutive androstane receptor. Biochem. Pharmacol. 2008, 76, 1288-1297
    • (2008) Biochem. Pharmacol. , vol.76 , pp. 1288-1297
    • Küblbeck, J.1    Jyrkkärinne, J.2    Poso, A.3    Turpeinen, M.4    Sippl, W.5    Honkakoski, P.6    Windshügel, B.7
  • 155
    • 41649107991 scopus 로고    scopus 로고
    • Structure-based virtual screening against SARS-3CL(pro) to identify novel non-peptidic hits
    • Mukherjee, P.; Desai, P.; Ross, L.; White, E.L.; Avery, M.A. Structure-based virtual screening against SARS-3CL(pro) to identify novel non-peptidic hits. Bioorg. Med. Chem. 2008, 16, 4138-4149.
    • (2008) Bioorg. Med. Chem. , vol.16 , pp. 4138-4149
    • Mukherjee, P.1    Desai, P.2    Ross, L.3    White, E.L.4    Avery, M.A.5
  • 157
    • 34548141774 scopus 로고    scopus 로고
    • Targeting plague virulence factors: A combined machine learning method and multiple conformational virtual screening for the discovery of Yersinia Protein Kinase A inhibitors
    • Hu, X.; Prehna, G.; Stebbins, C.E. Targeting plague virulence factors: A combined machine learning method and multiple conformational virtual screening for the discovery of Yersinia Protein Kinase A inhibitors. J. Med. Chem. 2007, 50, 3980-3983.
    • (2007) J. Med. Chem. , vol.50 , pp. 3980-3983
    • Hu, X.1    Prehna, G.2    Stebbins, C.E.3
  • 158
    • 34547692844 scopus 로고    scopus 로고
    • Novel virtual screening protocol based on the combined use of molecular modeling and electronion interaction potential techniques to design HIV-1 integrase inhibitors
    • Tintori, C.; Manetti, F.; Veljkovic, N.; Perovic, V.; Vercammen, J.; Hayes, S.; Massa, S.; Witvrouw, M.; Debyser, Z.; Veljkovic, V.; Botta, M. Novel virtual screening protocol based on the combined use of molecular modeling and electronion interaction potential techniques to design HIV-1 integrase inhibitors. J. Chem. Inf. Model. 2007, 47, 1536-1544.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1536-1544
    • Tintori, C.1    Manetti, F.2    Veljkovic, N.3    Perovic, V.4    Vercammen, J.5    Hayes, S.6    Massa, S.7    Witvrouw, M.8    Debyser, Z.9    Veljkovic, V.10    Botta, M.11
  • 160
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
    • Rush, T.S., 3rd; Grant, J.A.; Mosyak, L.; Nicholls, A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J. Med. Chem. 2005, 48, 1489-1495.
    • (2005) J. Med. Chem. , vol.48 , pp. 1489-1495
    • Rush, T.S.1    Grant, J.A.2    Mosyak, L.3    Nicholls, A.4
  • 161
    • 70349745554 scopus 로고    scopus 로고
    • Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity
    • Quintus, F.; Sperandio, O.; Grynberg, J.; Petitjean, M.; Tuffery, P. Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity. BMC Bioinformatics 2009, 10, 245.
    • (2009) BMC Bioinformatics , vol.10 , pp. 245
    • Quintus, F.1    Sperandio, O.2    Grynberg, J.3    Petitjean, M.4    Tuffery, P.5
  • 164
    • 67849106534 scopus 로고    scopus 로고
    • Wwligcsrre: A 3D ligand-based server for hit identification and optimization
    • Sperandio, O.; Petitjean, M.; Tuffery, P. Wwligcsrre: A 3D ligand-based server for hit identification and optimization. Nucleic Acids Res. 2009, 37, W504-509.
    • (2009) Nucleic Acids Res. , vol.37
    • Sperandio, O.1    Petitjean, M.2    Tuffery, P.3
  • 165
    • 50149103756 scopus 로고    scopus 로고
    • Synergies of virtual screening approaches
    • Muegge, I. Synergies of virtual screening approaches. Mini Rev. Med. Chem. 2008, 8, 927-933.
    • (2008) Mini Rev. Med. Chem. , vol.8 , pp. 927-933
    • Muegge, I.1
  • 167
    • 8544230644 scopus 로고    scopus 로고
    • Gasdock: A new approach for rapid flexible docking based on an improved multi-population genetic algorithm
    • Li, H.; Li, C.; Gui, C.; Luo, X.; Chen, K.; Shen, J.; Wang, X.; Jiang, H. Gasdock: A new approach for rapid flexible docking based on an improved multi-population genetic algorithm. Bioorg. Med. Chem. Lett. 2004, 14, 4671-4676.
    • (2004) Bioorg. Med. Chem. Lett. , vol.14 , pp. 4671-4676
    • Li, H.1    Li, C.2    Gui, C.3    Luo, X.4    Chen, K.5    Shen, J.6    Wang, X.7    Jiang, H.8
  • 168
    • 33750083590 scopus 로고    scopus 로고
    • Critical assessment of the automated AutoDock as a new docking tool for virtual screening
    • Park, H.; Lee, J.; Lee, S. Critical assessment of the automated AutoDock as a new docking tool for virtual screening. Proteins 2006, 65, 549-554.
    • (2006) Proteins , vol.65 , pp. 549-554
    • Park, H.1    Lee, J.2    Lee, S.3
  • 169
    • 6344294057 scopus 로고    scopus 로고
    • FlexX-Scan: Fast, structure-based virtual screening
    • Schellhammer, I.; Rarey, M. FlexX-Scan: Fast, structure-based virtual screening. Proteins 2004, 57, 504-517.
    • (2004) Proteins , vol.57 , pp. 504-517
    • Schellhammer, I.1    Rarey, M.2
  • 170
    • 31444441580 scopus 로고    scopus 로고
    • Surrogate docking: Structure-based virtual screening at high throughput speed
    • Yoon, S.; Smellie, A.; Hartsough, D.; Filikov, A. Surrogate docking: Structure-based virtual screening at high throughput speed. J. Comput. Aided Mol. Des. 2005, 19, 483-497.
    • (2005) J. Comput. Aided Mol. Des. , vol.19 , pp. 483-497
    • Yoon, S.1    Smellie, A.2    Hartsough, D.3    Filikov, A.4
  • 171
    • 37449004656 scopus 로고    scopus 로고
    • Molecular docking for substrate identification: The short-chain dehydrogenases/reductases
    • Favia, A.D.; Nobeli, I.; Glaser, F.; Thornton, J.M. Molecular docking for substrate identification: The short-chain dehydrogenases/reductases. J. Mol. Biol. 2008, 375, 855-874.
    • (2008) J. Mol. Biol. , vol.375 , pp. 855-874
    • Favia, A.D.1    Nobeli, I.2    Glaser, F.3    Thornton, J.M.4
  • 172
    • 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
  • 173
    • 1942471391 scopus 로고    scopus 로고
    • Assessing scoring functions for protein-ligand interactions
    • Ferrara, P.; Gohlke, H.; Price, D.J.; Klebe, G.; Brooks, C.L., 3rd. Assessing scoring functions for protein-ligand interactions. J. Med. Chem. 2004, 47, 3032-3047.
    • (2004) J. Med. Chem. , vol.47 , pp. 3032-3047
    • Ferrara, P.1    Gohlke, H.2    Price, D.J.3    Klebe, G.4    Brooks, C.L.5
  • 174
    • 33745714455 scopus 로고    scopus 로고
    • Assessing the discriminatory power of scoring functions for virtual screening
    • Seifert, M.H. Assessing the discriminatory power of scoring functions for virtual screening. J. Chem. Inf. Model. 2006, 46, 1456-1465.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1456-1465
    • Seifert, M.H.1
  • 175
    • 66149103553 scopus 로고    scopus 로고
    • Comparative assessment of scoring functions on a diverse test set
    • Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model. 2009, 49, 1079-1093.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1079-1093
    • Cheng, T.1    Li, X.2    Li, Y.3    Liu, Z.4    Wang, R.5
  • 176
    • 34447524011 scopus 로고    scopus 로고
    • Structure-based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections
    • Montes, M.; Miteva, M.A.; Villoutreix, B.O. Structure-based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections. Proteins 2007, 68, 712-725.
    • (2007) Proteins , vol.68 , pp. 712-725
    • Montes, M.1    Miteva, M.A.2    Villoutreix, B.O.3
  • 177
    • 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
  • 179
    • 41549086249 scopus 로고    scopus 로고
    • Consensus scoring with feature selection for structure-based virtual screening
    • Teramoto, R.; Fukunishi, H. Consensus scoring with feature selection 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
  • 181
    • 33748667774 scopus 로고    scopus 로고
    • Consensus scoring for protein-ligand interactions
    • Feher, M. Consensus scoring for protein-ligand interactions. Drug Discov. Today 2006, 11, 421-428.
    • (2006) Drug Discov. Today , vol.11 , pp. 421-428
    • Feher, M.1
  • 183
    • 33746867935 scopus 로고    scopus 로고
    • Gfscore: A general nonlinear consensus scoring function for high-throughput docking
    • Betzi, S.; Suhre, K.; Chetrit, B.; Guerlesquin, F.; Morelli, X. Gfscore: A general nonlinear consensus scoring function for high-throughput docking. J. Chem. Inf. Model. 2006, 46, 1704-1712.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1704-1712
    • Betzi, S.1    Suhre, K.2    Chetrit, B.3    Guerlesquin, F.4    Morelli, X.5
  • 184
    • 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
  • 186
    • 65249117481 scopus 로고    scopus 로고
    • Validation of molecular docking programs for virtual screening against dihydropteroate synthase
    • Hevener, K.E.; Zhao, W.; Ball, D.M.; Babaoglu, K.; Qi, J.; White, S.W.; Lee, R.E. Validation of molecular docking programs for virtual screening against dihydropteroate synthase. J. Chem. Inf. Model. 2009, 49, 444-460.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 444-460
    • Hevener, K.E.1    Zhao, W.2    Ball, D.M.3    Babaoglu, K.4    Qi, J.5    White, S.W.6    Lee, R.E.7
  • 187
    • 65449150253 scopus 로고    scopus 로고
    • An effective docking strategy for virtual screening based on multi-objective optimization algorithm
    • Li, H.; Zhang, H.; Zheng, M.; Luo, J.; Kang, L.; Liu, X.; Wang, X.; Jiang, H. An effective docking strategy for virtual screening based on multi-objective optimization algorithm. BMC Bioinformatics 2009, 10, 58.
    • (2009) BMC Bioinformatics , vol.10 , pp. 58
    • Li, H.1    Zhang, H.2    Zheng, M.3    Luo, J.4    Kang, L.5    Liu, X.6    Wang, X.7    Jiang, H.8
  • 188
    • 22244451417 scopus 로고    scopus 로고
    • Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes
    • Raha, K.; Merz, K.M., Jr. Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J. Med. Chem. 2005, 48, 4558-4575.
    • (2005) J. Med. Chem. , vol.48 , pp. 4558-4575
    • Raha, K.1    Merz Jr, K.M.2
  • 189
    • 39749175582 scopus 로고    scopus 로고
    • Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery
    • Fischer, B.; Fukuzawa, K.; Wenzel, W. Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery. Proteins 2008, 70, 1264-1273.
    • (2008) Proteins , vol.70 , pp. 1264-1273
    • Fischer, B.1    Fukuzawa, K.2    Wenzel, W.3
  • 191
    • 49449085235 scopus 로고    scopus 로고
    • Hot-spots-guided receptor-based pharmacophores (HS-Pharm): A knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores
    • Barillari, C.; Marcou, G.; Rognan, D. Hot-spots-guided receptor-based pharmacophores (HS-Pharm): A knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores. J. Chem. Inf. Model. 2008, 48, 1396-1410.
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1396-1410
    • Barillari, C.1    Marcou, G.2    Rognan, D.3
  • 192
    • 48149114539 scopus 로고    scopus 로고
    • Towards an integrated description of hydrogen bonding and dehydration: Decreasing false positives in virtual screening with the HYDE scoring function
    • Reulecke, I.; Lange, G.; Albrecht, J.; Klein, R.; Rarey, M. Towards an integrated description of hydrogen bonding and dehydration: Decreasing false positives in virtual screening with the HYDE scoring function. ChemMedChem 2008, 3, 885-897.
    • (2008) ChemMedChem , vol.3 , pp. 885-897
    • Reulecke, I.1    Lange, G.2    Albrecht, J.3    Klein, R.4    Rarey, M.5
  • 193
    • 77950862947 scopus 로고    scopus 로고
    • Post-docking virtual screening of diverse binding pockets: Comparative study using DOCK, AMMOS, X-score and FRED scoring functions
    • Pencheva, T.; Samna Soumana, O.; Pajeva, I.; Miteva, M.A. Post-docking virtual screening of diverse binding pockets: Comparative study using DOCK, AMMOS, X-score and FRED scoring functions. Eur. J. Med. Chem. 2010, doi:10.1016/j.ejmech.2009.12.025.
    • (2010) Eur. J. Med. Chem.
    • Pencheva, T.1    Samna Soumana, O.2    Pajeva, I.3    Miteva, M.A.4
  • 194
    • 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. Model. 2003, 9, 47-57.
    • (2003) J. Mol. Model. , vol.9 , pp. 47-57
    • Schulz-gasch, T.1    Stahl, M.2
  • 196
    • 33846889763 scopus 로고    scopus 로고
    • Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery
    • Catana, C.; Stouten, P.F. 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    Stouten, P.F.2
  • 197
    • 33244490820 scopus 로고    scopus 로고
    • Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
    • Huang, N.; Kalyanaraman, C.; Irwin, J.J.; Jacobson, M.P. Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening. J. Chem. Inf. Model. 2006, 46, 243-253.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 243-253
    • Huang, N.1    Kalyanaraman, C.2    Irwin, J.J.3    Jacobson, M.P.4
  • 198
    • 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 2004, 56, 235-249.
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 200
    • 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
  • 202
    • 0030466444 scopus 로고    scopus 로고
    • Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
    • Ladbury, J.E. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem. Biol. 1996, 3, 973-980.
    • (1996) Chem. Biol. , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 203
    • 33847655150 scopus 로고    scopus 로고
    • Classification of water molecules in protein binding sites
    • Barillari, C.; Taylor, J.; Viner, R.; Essex, J. W. Classification of water molecules in protein binding sites. J. Am. Chem. Soc. 2007, 129, 2577-2587.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 2577-2587
    • Barillari, C.1    Taylor, J.2    Viner, R.3    Essex, J.W.4
  • 204
    • 28144441347 scopus 로고    scopus 로고
    • Evaluating the Molecular Mechanics Poisson-Boltzmann Surface Area free energy method using a congeneric series of ligands to p38 MAP kinase
    • Pearlman, D.A. Evaluating the Molecular Mechanics Poisson-Boltzmann Surface Area free energy method using a congeneric series of ligands to p38 MAP kinase. J. Med. Chem. 2005, 48, 7796-7807.
    • (2005) J. Med. Chem. , vol.48 , pp. 7796-7807
    • Pearlman, D.A.1
  • 206
    • 0032562202 scopus 로고    scopus 로고
    • Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease
    • Louis, J.M.; Dyda, F.; Nashed, N.T.; Kimmel, A.R.; Davies, D.R. Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. Biochemistry 1998, 37, 2105-2110.
    • (1998) Biochemistry , vol.37 , pp. 2105-2110
    • Louis, J.M.1    Dyda, F.2    Nashed, N.T.3    Kimmel, A.R.4    Davies, D.R.5
  • 209
    • 58749097645 scopus 로고    scopus 로고
    • Dynamics of conserved waters in human Hsp90: Implications for drug design
    • Yan, A.; Grant, G.H.; Richards, W.G. Dynamics of conserved waters in human Hsp90: Implications for drug design. J. R. So.c Interface. 2008, 5 Suppl 3, S199-205.
    • (2008) J. R. So.c Interface. , vol.5 , Issue.SUPPL. 3
    • Yan, A.1    Grant, G.H.2    Richards, W.G.3
  • 211
    • 32344449937 scopus 로고    scopus 로고
    • Docking of aminoglycosides to hydrated and flexible RNA
    • Moitessier, N.; Westhof, E.; Hanessian, S. Docking of aminoglycosides to hydrated and flexible RNA. J. Med. Chem. 2006, 49, 1023-1033.
    • (2006) J. Med. Chem. , vol.49 , pp. 1023-1033
    • Moitessier, N.1    Westhof, E.2    Hanessian, S.3
  • 213
    • 0032961895 scopus 로고    scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey, M.; Kramer, B.; Lengauer, T. The particle concept: Placing discrete water molecules during protein-ligand docking predictions. Proteins 1999, 34, 17-28.
    • (1999) Proteins , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 214
    • 66149087635 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs
    • Corbeil, C.R.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs. J. Chem. Inf. Model. 2009, 49, 997-1009.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 997-1009
    • Corbeil, C.R.1    Moitessier, N.2
  • 215
    • 34547657456 scopus 로고    scopus 로고
    • Atypical protonation states in the active site of HIV-1 protease: A computational study
    • Czodrowski, P.; Sotriffer, C.A.; Klebe, G. Atypical protonation states in the active site of HIV-1 protease: A computational study. J. Chem. Inf. Model. 2007, 47, 1590-1598.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1590-1598
    • Czodrowski, P.1    Sotriffer, C.A.2    Klebe, G.3
  • 216
    • 35148897726 scopus 로고    scopus 로고
    • Tracing changes in protonation: A prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase
    • Steuber, H.; Czodrowski, P.; Sotriffer, C.A.; Klebe, G. Tracing changes in protonation: A prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase. J. Mol. Biol. 2007, 373, 1305-1320.
    • (2007) J. Mol. Biol. , vol.373 , pp. 1305-1320
    • Steuber, H.1    Czodrowski, P.2    Sotriffer, C.A.3    Klebe, G.4
  • 217
    • 54749089268 scopus 로고    scopus 로고
    • Protonation states of proteins and small molecules: Implications to ligand-receptor interactions
    • Mitra, R.; Shyam, R.; Mitra, I.; Miteva, M.A.; Alexov, E. Protonation states of proteins and small molecules: Implications to ligand-receptor interactions. Current Computer-Aided Drug Design 2008, 4, 169-179.
    • (2008) Current Computer-Aided Drug Design , vol.4 , pp. 169-179
    • Mitra, R.1    Shyam, R.2    Mitra, I.3    Miteva, M.A.4    Alexov, E.5
  • 220
    • 61949390938 scopus 로고    scopus 로고
    • Tautomer enumeration and stability prediction for virtual screening on large chemical databases
    • Milletti, F.; Storchi, L.; Sforna, G.; Cross, S.; Cruciani, G. Tautomer enumeration and stability prediction for virtual screening on large chemical databases. J. Chem. Inf. Model. 2009, 49, 68-75.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 68-75
    • Milletti, F.1    Storchi, L.2    Sforna, G.3    Cross, S.4    Cruciani, G.5
  • 221
    • 67650077383 scopus 로고    scopus 로고
    • Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results
    • ten Brink, T.; Exner, T.E. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J. Chem. Inf. Model. 2009, 49, 1535-1546.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1535-1546
    • Ten Brink, T.1    Exner, T.E.2
  • 222
    • 37249043664 scopus 로고    scopus 로고
    • Impact of ligand protonation on virtual screening against beta-secretase (BACE1)
    • Polgar, T.; Magyar, C.; Simon, I.; Keseru, G.M. Impact of ligand protonation on virtual screening against beta-secretase (BACE1). J. Chem. Inf. Model. 2007, 47, 2366-2373.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 2366-2373
    • Polgar, T.1    Magyar, C.2    Simon, I.3    Keseru, G.M.4
  • 223
    • 34249278087 scopus 로고    scopus 로고
    • Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
    • Rajamani, R.; Good, A.C. Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development. Curr. Opin. Drug Discov. Devel. 2007, 10, 308-315.
    • (2007) Curr. Opin. Drug Discov. Devel. , vol.10 , pp. 308-315
    • Rajamani, R.1    Good, A.C.2
  • 224
  • 225
    • 24344456625 scopus 로고    scopus 로고
    • Study of the insulin dimerization: Binding free energy calculations and per-residue free energy decomposition
    • Zoete, V.; Meuwly, M.; Karplus, M. Study of the insulin dimerization: Binding free energy calculations and per-residue free energy decomposition. Proteins 2005, 61, 79-93.
    • (2005) Proteins , vol.61 , pp. 79-93
    • Zoete, V.1    Meuwly, M.2    Karplus, M.3


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