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Volumn 7, Issue 4, 2008, Pages 833-852

Pose scaling: Geometrical assessment of ligand binding poses

Author keywords

Binding pose; Binding site; Docking; Geometrical match; Scoring function

Indexed keywords


EID: 51449094597     PISSN: 02196336     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219633608004155     Document Type: Article
Times cited : (4)

References (51)
  • 1
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
    • Leach AR, Shoichet BK, Peishoff CE, Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps, J Med Chem 49:5851-5855, 2006.
    • (2006) J Med Chem , vol.49 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 2
    • 33846094031 scopus 로고    scopus 로고
    • Computational identification of inhibitors of protein-protein interactions
    • Zhong S, Macias AT, MacKerell AD, Jr, Computational identification of inhibitors of protein-protein interactions, Curr Top Med Chem 7:63-82, 2007.
    • (2007) Curr Top Med Chem , vol.7 , pp. 63-82
    • Zhong, S.1    Macias, A.T.2    MacKerell Jr, A.D.3
  • 3
    • 39049090620 scopus 로고    scopus 로고
    • Theoretical and practical considerations in virtual screening: A beaten field?
    • Kontoyianni M, Madhav P, Suchanek E, Seibel W, Theoretical and practical considerations in virtual screening: A beaten field? Curr Med Chem 15:107-116, 2008.
    • (2008) Curr Med Chem , vol.15 , pp. 107-116
    • Kontoyianni, M.1    Madhav, P.2    Suchanek, E.3    Seibel, W.4
  • 5
    • 33747458480 scopus 로고    scopus 로고
    • Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease
    • Lu IL, Mahindroo N, Liang PH, Peng YH, Kuo CJ, Tsai KC, Hsieh HP, Chao YS, Wu SY, Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease, J Med Chem 49:5154-5161, 2006.
    • (2006) J Med Chem , vol.49 , pp. 5154-5161
    • Lu, I.L.1    Mahindroo, N.2    Liang, P.H.3    Peng, Y.H.4    Kuo, C.J.5    Tsai, K.C.6    Hsieh, H.P.7    Chao, Y.S.8    Wu, S.Y.9
  • 6
    • 34548082362 scopus 로고    scopus 로고
    • Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: Novel antimicrobial targets
    • Furci LM, Lopes P, Eakanunkul S, Zhong S, MacKerell AD, Jr, Wilks A, Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: Novel antimicrobial targets, J Med Chem 50:3804-3813, 2007.
    • (2007) J Med Chem , vol.50 , pp. 3804-3813
    • Furci, L.M.1    Lopes, P.2    Eakanunkul, S.3    Zhong, S.4    MacKerell Jr, A.D.5    Wilks, A.6
  • 7
    • 3042590341 scopus 로고    scopus 로고
    • Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY+3 binding site
    • Huang N, Nagarsekar A, Xia GJ, Hayashi J, MacKerell AD, Jr, Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY+3 binding site, J Med Chem 47:3502-3511, 2004.
    • (2004) J Med Chem , vol.47 , pp. 3502-3511
    • Huang, N.1    Nagarsekar, A.2    Xia, G.J.3    Hayashi, J.4    MacKerell Jr, A.D.5
  • 9
    • 35548942306 scopus 로고    scopus 로고
    • Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models
    • Bowman AL, Nikolovska-Coleska Z, Zhong H, Wang S, Carlson HA, Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models, J Am Chem Soc 129:12809-12814, 2007.
    • (2007) J Am Chem Soc , vol.129 , pp. 12809-12814
    • Bowman, A.L.1    Nikolovska-Coleska, Z.2    Zhong, H.3    Wang, S.4    Carlson, H.A.5
  • 10
    • 33749506205 scopus 로고    scopus 로고
    • Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
    • Laurie AT, Jackson RM, Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening, Curr Protein Pept Sci 7:395-406, 2006.
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 395-406
    • Laurie, A.T.1    Jackson, R.M.2
  • 11
    • 37249062102 scopus 로고    scopus 로고
    • Binding response: A descriptor for selecting ligand binding site on protein surfaces
    • Zhong S, MacKerell AD, Jr, Binding response: A descriptor for selecting ligand binding site on protein surfaces, J Chem Inf Model 47:2303-2315, 2007.
    • (2007) J Chem Inf Model , vol.47 , pp. 2303-2315
    • Zhong, S.1    MacKerell Jr, A.D.2
  • 12
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M, Skolnick J, A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation, Proc Natl Acad Sci USA 105:129-134, 2008.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 13
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R, Principles of docking: An overview of search algorithms and a guide to scoring functions, Proteins 47:409-443, 2002.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 15
    • 38149088192 scopus 로고    scopus 로고
    • Flexible ligand-flexible protein docking in protein kinase systems
    • Wong CF, Flexible ligand-flexible protein docking in protein kinase systems, Biochim Biophys Acta 1784:244-251, 2008.
    • (2008) Biochim Biophys Acta , vol.1784 , pp. 244-251
    • Wong, C.F.1
  • 16
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDB-bind refined set of 800 protein-ligand complexes
    • Wang R, Lu Y, Fang X, Wang S, An extensive test of 14 scoring functions using the PDB-bind refined set of 800 protein-ligand complexes, J Chem Inf Comput Sci 44:2114-2125, 2004.
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 2114-2125
    • Wang, R.1    Lu, Y.2    Fang, X.3    Wang, S.4
  • 17
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • Jain AN, Scoring functions for protein-ligand docking, Curr Protein Pept Sci 7:407- 420, 2006.
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 407-420
    • Jain, A.N.1
  • 18
    • 34249278087 scopus 로고    scopus 로고
    • Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
    • Rajamani R, Good AC, Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development, Curr Opin Drug Discov Devel 10:308-315, 2007.
    • (2007) Curr Opin Drug Discov Devel , vol.10 , pp. 308-315
    • Rajamani, R.1    Good, A.C.2
  • 19
    • 0037208312 scopus 로고    scopus 로고
    • Consideration of molecular weight during compound selection in virtual target-based database screening
    • Pan Y, Huang N, Cho S, MacKerell AD, Jr, Consideration of molecular weight during compound selection in virtual target-based database screening, J Chem Inf Comput Sci 43:267-272, 2003.
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 267-272
    • Pan, Y.1    Huang, N.2    Cho, S.3    MacKerell Jr, A.D.4
  • 20
    • 13244266921 scopus 로고    scopus 로고
    • Lead- and drug-like compounds: The rule-of-five revolution
    • Lipinski CA, Lead- and drug-like compounds: The rule-of-five revolution, Drug Discovery Today: Technologies 1:337-341, 2004.
    • (2004) Drug Discovery Today: Technologies , vol.1 , pp. 337-341
    • Lipinski, C.A.1
  • 21
    • 33644861784 scopus 로고    scopus 로고
    • Diversity in medicinal chemistry space
    • Gorse AD, Diversity in medicinal chemistry space, Curr Top Med Chem 6:3-18, 2006.
    • (2006) Curr Top Med Chem , vol.6 , pp. 3-18
    • Gorse, A.D.1
  • 25
    • 6344294057 scopus 로고    scopus 로고
    • Schellhammer I, Rarey M, FlexX-Scan: Fast, structure-based virtual screening, Proteins 57:504-517, 2004.
    • Schellhammer I, Rarey M, FlexX-Scan: Fast, structure-based virtual screening, Proteins 57:504-517, 2004.
  • 28
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang C, Liu S, Zhu Q, Zhou Y, A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes, J Med Chem 48:2325-2335, 2005.
    • (2005) J Med Chem , vol.48 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 29
    • 33749242403 scopus 로고    scopus 로고
    • Muegge I, J Med Chem 49:5895-5902, 2006.
    • (2006) J Med Chem , vol.49 , pp. 5895-5902
    • Muegge, I.1
  • 30
    • 33749239216 scopus 로고    scopus 로고
    • A knowledge-based potential scoring function accounting for protein atom mobility
    • Yang CY, Wang R, Wang S, M-score: A knowledge-based potential scoring function accounting for protein atom mobility, J Med Chem 49:5903-5911, 2006.
    • (2006) J Med Chem , vol.49 , pp. 5903-5911
    • Yang, C.Y.1    Wang, R.2    Wang, S.3    M-score4
  • 31
    • 33244478322 scopus 로고    scopus 로고
    • Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes
    • Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S, Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes, J Chem Inf Model 46:380-391, 2006.
    • (2006) J Chem Inf Model , vol.46 , pp. 380-391
    • Oda, A.1    Tsuchida, K.2    Takakura, T.3    Yamaotsu, N.4    Hirono, S.5
  • 32
    • 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 48:288-295, 2008.
    • (2008) J Chem Inf Model , vol.48 , pp. 288-295
    • Teramoto, R.1    Fukunishi, H.2
  • 33
    • 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 37:228-241, 1999.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 34
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing TJ, Makino S, Skillman AG, Kuntz ID, DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases, J Comput Aided Mol Des 15:411-428, 2001.
    • (2001) J Comput Aided Mol Des , vol.15 , pp. 411-428
    • Ewing, T.J.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 35
    • 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 25:412-422, 2004.
    • (2004) J Comput Chem , vol.25 , pp. 412-422
    • Cecchini, M.1    Kolb, P.2    Majeux, N.3    Caflisch, A.4
  • 36
    • 85135598892 scopus 로고    scopus 로고
    • Liu M, Wang S, MCDOCK: A Monte Carlo simulation approach to the molecular docking problem, J Comput Aided Mol Des 13:435-451, 1999.
    • Liu M, Wang S, MCDOCK: A Monte Carlo simulation approach to the molecular docking problem, J Comput Aided Mol Des 13:435-451, 1999.
  • 37
    • 34548672784 scopus 로고    scopus 로고
    • An all atom energy based Monte Carlo docking protocol for protein-ligand complexes
    • ParDOCK
    • Gupta A, Gandhimathi A, Sharma P, Jayaram B, ParDOCK: An all atom energy based Monte Carlo docking protocol for protein-ligand complexes, Protein Pept Lett 14:632-646, 2007.
    • (2007) Protein Pept Lett , vol.14 , pp. 632-646
    • Gupta, A.1    Gandhimathi, A.2    Sharma, P.3    Jayaram, B.4
  • 39
    • 0036022961 scopus 로고    scopus 로고
    • A probabilistic method for docking molecular fragments by sampling low energy conformational space
    • Jackson RM, Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space, J Comput Aided Mol Des 16:43-57, 2002.
    • (2002) J Comput Aided Mol Des , vol.16 , pp. 43-57
    • Jackson, R.M.1    Q-fit2
  • 40
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M, Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy, J Med Chem 47:45-55, 2004.
    • (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
  • 41
  • 43
    • 0029967679 scopus 로고    scopus 로고
    • Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution
    • Tong L, Warren TC, King J, Betageri R, Rose J, Jakes S, Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution, J Mol Biol 256:601-610, 1996.
    • (1996) J Mol Biol , vol.256 , pp. 601-610
    • Tong, L.1    Warren, T.C.2    King, J.3    Betageri, R.4    Rose, J.5    Jakes, S.6
  • 44
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards FM, Areas, volumes, packing and protein structure, Annu Rev Biophys Bio-eng 6:151-176, 1977.
    • (1977) Annu Rev Biophys Bio-eng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 45
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly M, Analytical molecular surface calculation, J Appl Cryst 16:548-558, 1983.
    • (1983) J Appl Cryst , vol.16 , pp. 548-558
    • Connolly, M.1
  • 46
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly ML, Solvent-accessible surfaces of proteins and nucleic acids, Science 221:709-713, 1983.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 50
    • 0036084259 scopus 로고    scopus 로고
    • Efficient docking of peptides to proteins without prior knowledge of the binding site
    • Hetenyi C, van der Spoel D, Efficient docking of peptides to proteins without prior knowledge of the binding site, Protein Sci 11:1729-1737, 2002.
    • (2002) Protein Sci , vol.11 , pp. 1729-1737
    • Hetenyi, C.1    van der Spoel, D.2
  • 51
    • 32344440995 scopus 로고    scopus 로고
    • Blind docking of drug-sized compounds to proteins with up to a thousand residues
    • Hetenyi C, van der Spoel D, Blind docking of drug-sized compounds to proteins with up to a thousand residues, FEBS Lett 580:1447-1450, 2006.
    • (2006) FEBS Lett , vol.580 , pp. 1447-1450
    • Hetenyi, C.1    van der Spoel, D.2


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