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Volumn 18, Issue 11, 2012, Pages 4843-4863

Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors

Author keywords

Anticancer; dbCICA; Docking; Heat shock protein 90 ; LigandFit

Indexed keywords

ADENOSINE TRIPHOSPHATASE; AMINO ACID; HEAT SHOCK PROTEIN 90; HEAT SHOCK PROTEIN 90 INHIBITOR;

EID: 84870477772     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1479-z     Document Type: Article
Times cited : (36)

References (95)
  • 4
    • 0043288724 scopus 로고    scopus 로고
    • Heat shock protein 90 as a molecular target for cancer therapeutics
    • Isaacs JS, Xu W, Neckers L (2003) Heat shock protein 90 as a molecular target for cancer therapeutics. Cancer Cell 3:213-217.
    • (2003) Cancer Cell , vol.3 , pp. 213-217
    • Isaacs, J.S.1    Xu, W.2    Neckers, L.3
  • 5
    • 41149111451 scopus 로고    scopus 로고
    • The Hsp90α molecular chaperone: An open and shut case for treatment
    • Pearl LH, Prodromou C, Workman P (2008) The Hsp90α molecular chaperone: an open and shut case for treatment. Biochem J 41:439-453.
    • (2008) Biochem J , vol.41 , pp. 439-453
    • Pearl, L.H.1    Prodromou, C.2    Workman, P.3
  • 6
    • 0033502429 scopus 로고    scopus 로고
    • Geldanamycin as a potential anti-cancer agent: Its molecular target and biochemical activity
    • Neckers L, Schulte TW, Mimnaugh E (1999) Geldanamycin as a potential anti-cancer agent: its molecular target and biochemical activity. Invest New Drugs 17:361-373.
    • (1999) Invest New Drugs , vol.17 , pp. 361-373
    • Neckers, L.1    Schulte, T.W.2    Mimnaugh, E.3
  • 8
    • 38849117688 scopus 로고    scopus 로고
    • Discovery and development of purine scaffold Hsp90α inhibitors
    • Chiosis G, Kang Y, Sun W (2008) Discovery and development of purine scaffold Hsp90α inhibitors. Expert Opin Drug Discov 3:99-114.
    • (2008) Expert Opin Drug Discov , vol.3 , pp. 99-114
    • Chiosis, G.1    Kang, Y.2    Sun, W.3
  • 9
    • 35148840116 scopus 로고    scopus 로고
    • A novel class of Hsp90α inhibitors isolated by structure-based virtual screening
    • Hwangseo P, Yun-Jung K, Ji-Sook H (2007) A novel class of Hsp90α inhibitors isolated by structure-based virtual screening. Bioorg Med Chem Lett 17:6345-6349.
    • (2007) Bioorg Med Chem Lett , vol.17 , pp. 6345-6349
    • Hwangseo, P.1    Yun-Jung, K.2    Ji-Sook, H.3
  • 12
    • 0036836964 scopus 로고    scopus 로고
    • Development of a purine-scaffold novel vlass of Hsp90α binders that inhibit the proliferation of cancer cells and induce the degradation of Her2tyrosine kinase
    • Chiosis G, Lucas B, Shtil A, Huezoa H, Rosen N (2002) Development of a purine-scaffold novel vlass of Hsp90α binders that inhibit the proliferation of cancer cells and induce the degradation of Her2tyrosine kinase. Bioorg Med Chem 10:3555-3564.
    • (2002) Bioorg Med Chem , vol.10 , pp. 3555-3564
    • Chiosis, G.1    Lucas, B.2    Shtil, A.3    Huezoa, H.4    Rosen, N.5
  • 13
    • 33746379315 scopus 로고    scopus 로고
    • Using natural product inhibitors to validate Hsp90α as a molecular target in cancer
    • Neckers L (2006) Using natural product inhibitors to validate Hsp90α as a molecular target in cancer. Curr Top Med Chem 6:1163-1171.
    • (2006) Curr Top Med Chem , vol.6 , pp. 1163-1171
    • Neckers, L.1
  • 14
    • 33749507014 scopus 로고    scopus 로고
    • Effectiveness of Hsp90α inhibitors as anti-cancer drugs
    • Xiao L, Lu X, Ruden DM (2006) Effectiveness of Hsp90α inhibitors as anti-cancer drugs. Mini-Rev Med Chem 6:1137-1143.
    • (2006) Mini-Rev Med Chem , vol.6 , pp. 1137-1143
    • Xiao, L.1    Lu, X.2    Ruden, D.M.3
  • 15
    • 65549138976 scopus 로고    scopus 로고
    • The complex dance of the molecular chaperone Hsp90
    • Neckers L, Mollapour M, Tsutsumi S (2009) The complex dance of the molecular chaperone Hsp90. Trends Biochem Sci 34:223-226.
    • (2009) Trends Biochem Sci , vol.34 , pp. 223-226
    • Neckers, L.1    Mollapour, M.2    Tsutsumi, S.3
  • 17
    • 79953167563 scopus 로고    scopus 로고
    • Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMTand GP inhibitors as case studies
    • Taha MO, Habash M, Al-Hadidi Z, Al-Bakri A, Younis K, Sisan S (2011) Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMTand GP inhibitors as case studies. J Chem Inf Model 51:647-669.
    • (2011) J Chem Inf Model , vol.51 , pp. 647-669
    • Taha, M.O.1    Habash, M.2    Al-Hadidi, Z.3    Al-Bakri, A.4    Younis, K.5    Sisan, S.6
  • 19
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • Kontoyianni M, McClellan LM, Sokol GS (2004) Evaluation of docking performance: comparative data on docking algorithms. J Med Chem 47:558-565.
    • (2004) J Med Chem , vol.47 , pp. 558-565
    • Kontoyianni, M.1    Mcclellan, L.M.2    Sokol, G.S.3
  • 20
    • 77950207644 scopus 로고    scopus 로고
    • Tackling the challenges posed by target flexibility in drug design
    • Beier C, Zacharias M (2010) Tackling the challenges posed by target flexibility in drug design. Expert Opin Drug Dis 5:347-359.
    • (2010) Expert Opin Drug Dis , vol.5 , pp. 347-359
    • Beier, C.1    Zacharias, M.2
  • 21
    • 79953203460 scopus 로고    scopus 로고
    • FlexX suite
    • Boyd S (2007) FlexX suite. Chem World UK 4:72.
    • (2007) Chem World UK , vol.4 , pp. 72
    • Boyd, S.1
  • 22
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489.
    • (1996) J Mol Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 23
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing TJA, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aid Mol Des 15:411-428.
    • (2001) J Comput Aid Mol des , vol.15 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 24
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 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
  • 28
  • 29
    • 84870533337 scopus 로고    scopus 로고
    • Accelrys Inc., Accelrys Inc. San Diego
    • Accelrys Inc. (2000) Cerius2 LigandFit 4.10. Accelrys Inc., San Diego.
    • (2000) Cerius2 LigandFit 4.10
  • 30
    • 0035342434 scopus 로고    scopus 로고
    • High throughput docking for library design and library prioritization
    • Diller DJ, Merz KM (2001) High throughput docking for library design and library prioritization. Proteins 43:113-124.
    • (2001) Proteins , vol.43 , pp. 113-124
    • Diller, D.J.1    Merz, K.M.2
  • 31
    • 65749110436 scopus 로고    scopus 로고
    • Computational intelligence methods for docking scores
    • Hecht D, Fogel GB (2009) Computational intelligence methods for docking scores. Curr Comput Aid Drug 5:56-68.
    • (2009) Curr Comput Aid Drug , vol.5 , pp. 56-68
    • Hecht, D.1    Fogel, G.B.2
  • 32
    • 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 (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 43:4759-4767.
    • (2000) J Med Chem , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 33
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Gao WR, Lai YL (1998) SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model 4:379-394.
    • (1998) J Mol Model , vol.4 , pp. 379-394
    • Gao, W.R.1    Lai, Y.L.2
  • 35
    • 26444588137 scopus 로고    scopus 로고
    • Drug score-knowledgebased scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
    • Velec HFG, Gohlke H, Klebe G (2005) Drug score-knowledgebased scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 48:6296-6303.
    • (2005) J Med Chem , vol.48 , pp. 6296-6303
    • Velec, H.F.G.1    Gohlke, H.2    Klebe, G.3
  • 36
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • Jain AN (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7:407-420.
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 407-420
    • Jain, A.N.1
  • 37
    • 34249278087 scopus 로고    scopus 로고
    • Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
    • Rajamani R, Good AC (2007) Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development. Curr Opin Drug Disc 10:308-315.
    • (2007) Curr Opin Drug Disc , vol.10 , pp. 308-315
    • Rajamani, R.1    Good, A.C.2
  • 38
    • 2942720960 scopus 로고    scopus 로고
    • Impact of scoring functions on enrichment in docking- based virtual screening: An application study on renin inhibitors
    • Krovat EM, Langer T (2004) Impact of scoring functions on enrichment in docking- based virtual screening: an application study on renin inhibitors. J Chem Inf Comput Sci 44:1123-1129.
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 1123-1129
    • Krovat, E.M.1    Langer, T.2
  • 39
    • 33845335781 scopus 로고    scopus 로고
    • Towards predictive ligand design with free-energy based computational methods?
    • Foloppe N, Hubbard R (2006) Towards predictive ligand design with free-energy based computational methods? Curr Med Chem 13:3583-3608.
    • (2006) Curr Med Chem , vol.13 , pp. 3583-3608
    • Foloppe, N.1    Hubbard, R.2
  • 40
    • 67650077384 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules
    • Are popular scoring functions accurate for this class of proteins?
    • Englebienne P, Moitessier N (2009) Docking ligands into flexible and solvated macromolecules. Are popular scoring functions accurate for this class of proteins? J Chem Inf Model 49:1568-1580.
    • (2009) J Chem Inf Model , vol.49 , pp. 1568-1580
    • Englebienne, P.1    Moitessier, N.2
  • 41
    • 0030255303 scopus 로고    scopus 로고
    • Scoring non-covalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • Jain AN (1996) Scoring non-covalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des 10:427-440.
    • (1996) J Comput Aided Mol des , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 42
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    • Böhm HJ (1998) Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 12:309-323.
    • (1998) J Comput Aided Mol des , vol.12 , pp. 309-323
    • Böhm, H.J.1
  • 43
    • 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 MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) 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 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
  • 44
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang R, Gao Y, Lai L (1998) SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model 4:379-394.
    • (1998) J Mol Model , vol.4 , pp. 379-394
    • Wang, R.1    Gao, Y.2    Lai, L.3
  • 45
    • 0039012103 scopus 로고    scopus 로고
    • Reduced dimensionality in ligand-protein structure prediction: Covalent inhibitors of serine proteases and design of site-directed combinatorial libraries
    • Parrill L, Rami Reddy M (eds), American Chemical Society, Washington, DC
    • Gehlhaar DK, Bouzida D, Rejto P (1999) Reduced dimensionality in ligand-protein structure prediction: covalent inhibitors of serine proteases and design of site-directed combinatorial libraries. In: Parrill L, Rami Reddy M (eds) Rational drug design: novel methodology and practical applications. American Chemical Society, Washington, DC, pp 292-311.
    • (1999) Rational Drug Design: Novel Methodology and Practical Applications , pp. 292-311
    • Gehlhaar, D.K.1    Bouzida, D.2    Rejto, P.3
  • 46
    • 0036022960 scopus 로고    scopus 로고
    • Further development and of empirical scoring functions for structure-based binding validation affinity prediction
    • Wang R, Lai L, Wang S (2002) Further development and of empirical scoring functions for structure-based binding validation affinity prediction. J Comput Aided Mol Des 16:11-26.
    • (2002) J Comput Aided Mol des , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 47
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 42:791-804.
    • (1999) J Med Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 48
    • 0033673508 scopus 로고    scopus 로고
    • A knowledge-based scoring function for protein- ligand interactions: Probing the reference state
    • Muegge I (2000) A knowledge-based scoring function for protein- ligand interactions: probing the reference state. Perspect Drug Discov 20:99-114.
    • (2000) Perspect Drug Discov , vol.20 , pp. 99-114
    • Muegge, I.1
  • 49
    • 0001745748 scopus 로고    scopus 로고
    • Effect of ligand volume correction on PMF scoring
    • Muegge I (2001) Effect of ligand volume correction on PMF scoring. J Comput Chem 22:418-425.
    • (2001) J Comput Chem , vol.22 , pp. 418-425
    • Muegge, I.1
  • 50
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 295:337-356.
    • (2000) J Mol Biol , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 51
    • 33749242403 scopus 로고    scopus 로고
    • PMF scoring revisited
    • Muegge I (2006) PMF scoring revisited. J Med Chem 49:5895- 5902.
    • (2006) J Med Chem , vol.49 , pp. 5895-5902
    • Muegge, I.1
  • 52
    • 69249141491 scopus 로고    scopus 로고
    • Recent advances in computeraided drug design
    • Song CM, Lim SJ, Tong JC (2009) Recent advances in computeraided drug design. Brief Bioinform 10:579-591.
    • (2009) Brief Bioinform , vol.10 , pp. 579-591
    • Song, C.M.1    Lim, S.J.2    Tong, J.C.3
  • 53
    • 67649225348 scopus 로고    scopus 로고
    • Efficient drug lead discovery and optimization
    • Jorgensen WL (2009) Efficient drug lead discovery and optimization. Acc Chem Res 42:724-733.
    • (2009) Acc Chem Res , vol.42 , pp. 724-733
    • Jorgensen, W.L.1
  • 54
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein- ligand interactions
    • Docking and scoring: Successes and gaps
    • Leach AR, Shoichet BK, Peishoff CE (2006) Prediction of protein- ligand interactions. Docking and scoring: successes and gaps. J Med Chem 49:5851-5855.
    • (2006) J Med Chem , vol.49 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 55
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • Klebe G (2006) Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 11:580-594.
    • (2006) Drug Discov Today , vol.11 , pp. 580-594
    • Klebe, G.1
  • 56
    • 72449167058 scopus 로고    scopus 로고
    • Crystal contacts as nature's docking solutions
    • Krissinel E (2009) Crystal contacts as nature's docking solutions. J Comput Chem 31:133-143.
    • (2009) J Comput Chem , vol.31 , pp. 133-143
    • Krissinel, E.1
  • 57
    • 77950650980 scopus 로고    scopus 로고
    • Towards accurate free energy calculations in ligand protein-binding studies
    • Steinbrecher T, Labahn A (2010) Towards accurate free energy calculations in ligand protein-binding studies. Curr Med Chem 17:767-785.
    • (2010) Curr Med Chem , vol.17 , pp. 767-785
    • Steinbrecher, T.1    Labahn, A.2
  • 58
    • 29144472246 scopus 로고    scopus 로고
    • Effects of variable docking conditions and scoring functions on the qualities of protein aligned CoMFA models constructed from diverse h-PTP 1B inhibitors
    • Taha MO, AlDhamin M (2005) Effects of variable docking conditions and scoring functions on the qualities of protein aligned CoMFA models constructed from diverse h-PTP 1B inhibitors. J Med Chem 48:8016-8034.
    • (2005) J Med Chem , vol.48 , pp. 8016-8034
    • Taha, M.O.1    Aldhamin, M.2
  • 59
    • 0032993815 scopus 로고    scopus 로고
    • Scoring functions: A view from the bench
    • Tame JRH (1999) Scoring functions: a view from the bench. J Comput Aided Mol Des 13:99-108.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 99-108
    • Tame, J.R.H.1
  • 60
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 93:2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 61
    • 34447108978 scopus 로고    scopus 로고
    • Water, water everywhere-except where it matters
    • Homans SW (2007) Water, water everywhere-except where it matters. Drug Discov Today 12:534-539.
    • (2007) Drug Discov Today , vol.12 , pp. 534-539
    • Homans, S.W.1
  • 62
    • 0029450365 scopus 로고
    • Hydration in drug design
    • 1.Multiple hydrogen-bonding features of water molecules in mediating protein- ligand interactions
    • Poornima CS, Dean PM (1995) Hydration in drug design. 1.Multiple hydrogen-bonding features of water molecules in mediating protein- ligand interactions. J Comput Aided Mol Des 9:500-512.
    • (1995) J Comput Aided Mol des , vol.9 , pp. 500-512
    • Poornima, C.S.1    Dean, P.M.2
  • 63
    • 0029444719 scopus 로고
    • Hydration in drug design
    • 2. Influence of local site surface shape on water binding
    • Poornima CS, Dean PM (1995) Hydration in drug design. 2. Influence of local site surface shape on water binding. J Comput Aided Mol Des 9:513-520.
    • (1995) J Comput Aided Mol des , vol.9 , pp. 513-520
    • Poornima, C.S.1    Dean, P.M.2
  • 64
    • 0029450636 scopus 로고
    • Hydration in drug design
    • 3. Conserved water molecules at the ligand-binding sites of homologous proteins
    • Poornima CS, Dean PM (1995) Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins. J Comput Aided Mol Des 9:521-531.
    • (1995) J Comput Aided Mol des , vol.9 , pp. 521-531
    • Poornima, C.S.1    Dean, P.M.2
  • 66
    • 0031442549 scopus 로고    scopus 로고
    • A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure-activity relationship analysis
    • Pastor M, Cruciani G, Watson K (1997) A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure-activity relationship analysis. J Med Chem 40:4089-4102.
    • (1997) J Med Chem , vol.40 , pp. 4089-4102
    • Pastor, M.1    Cruciani, G.2    Watson, K.3
  • 68
    • 29144505998 scopus 로고    scopus 로고
    • New methods for structure-based de novo drug design
    • Harvey AL (ed), Wiley, Chichester
    • Waszkowycz B (1998) New methods for structure-based de novo drug design. In: Harvey AL (ed) Advances in drug discovery techniques. Wiley, Chichester, pp 150-153.
    • (1998) Advances in Drug Discovery Techniques , pp. 150-153
    • Waszkowycz, B.1
  • 69
    • 37249031360 scopus 로고    scopus 로고
    • Lessons in molecular recognition
    • 2. Assessing and improving crossdocking accuracy
    • Sutherland JJ, Nandigam RK, Erickson JA, Vieth M (2007) Lessons in molecular recognition. 2. Assessing and improving crossdocking accuracy. J Chem Inf Model 47:2293-2302.
    • (2007) J Chem Inf Model , vol.47 , pp. 2293-2302
    • Sutherland, J.J.1    Nandigam, R.K.2    Erickson, J.A.3    Vieth, M.4
  • 71
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46:2287-2303.
    • (2003) J Med Chem , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 72
    • 34548289768 scopus 로고    scopus 로고
    • Combining docking, scoring and molecular field analyses to probe influenza neuraminidase- ligand interactions
    • Abu-Hammad AM, Afifi F, Taha MO (2007) Combining docking, scoring and molecular field analyses to probe influenza neuraminidase- ligand interactions. J Mol Graph Model 26:443-456.
    • (2007) J Mol Graph Model , vol.26 , pp. 443-456
    • Abu-Hammad, A.M.1    Afifi, F.2    Taha, M.O.3
  • 73
    • 64249106202 scopus 로고    scopus 로고
    • Homology modeling of MCH1 receptor and validation by docking/scoring and protein-aligned CoMFA
    • Abu-Hammad A, Zalloum WA, Zalloum H, Abu-Sheikha G, Taha MO (2009) Homology modeling of MCH1 receptor and validation by docking/scoring and protein-aligned CoMFA. Eur J Med Chem 44:2583-2596.
    • (2009) Eur J Med Chem , vol.44 , pp. 2583-2596
    • Abu-Hammad, A.1    Zalloum, W.A.2    Zalloum, H.3    Abu-Sheikha, G.4    Taha, M.O.5
  • 74
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam CM, Jiang X, Oldfield T, Waldman M (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 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
  • 75
  • 78
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity- A rapid access to atomic charges
    • Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 36:3219-3228.
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 79
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST (1995) Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem Biol 2:317-324.
    • (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
  • 80
    • 84861335128 scopus 로고    scopus 로고
    • Accelrys Inc., Accelrys Inc. San Diego
    • Accelrys Inc. (2009) Discovery Studio 2.5. Accelrys Inc., San Diego.
    • (2009) Discovery Studio 2.5
  • 81
    • 33749239830 scopus 로고    scopus 로고
    • Discovery of potent inhibitors of pseudomonal quorum sensing via pharmacophore modeling and in silico screening
    • Taha MO, Al-Bakri AG, Zalloum WA (2006) Discovery of potent inhibitors of pseudomonal quorum sensing via pharmacophore modeling and in silico screening. Bioorg Med Chem Lett 16:5902-5906.
    • (2006) Bioorg Med Chem Lett , vol.16 , pp. 5902-5906
    • Taha, M.O.1    Al-Bakri, A.G.2    Zalloum, W.A.3
  • 82
    • 33846794737 scopus 로고    scopus 로고
    • Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening
    • Taha MO, Bustanji Y, Al-Bakri AG, Al-Motassem Y, Zalloum WA, Al-Masri IM, Atallah N (2007) Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening. J Mol Graph Model 25:870-884.
    • (2007) J Mol Graph Model , vol.25 , pp. 870-884
    • Taha, M.O.1    Bustanji, Y.2    Al-Bakri, A.G.3    Al-Motassem, Y.4    Zalloum, W.A.5    Al-Masri, I.M.6    Atallah, N.7
  • 85
    • 30344445980 scopus 로고    scopus 로고
    • Development and optimization of a useful assay for determining Hsp90s inherent ATPase activity
    • Christopher A, Boris AK, Brian SJ (2006) Development and optimization of a useful assay for determining Hsp90s inherent ATPase activity. Bioorg Med Chem 14:1134-1142.
    • (2006) Bioorg Med Chem , vol.14 , pp. 1134-1142
    • Christopher, A.1    Boris, A.K.2    Brian, S.J.3
  • 86
    • 80052837394 scopus 로고    scopus 로고
    • Some sulfonamide drugs inhibit AT pase activity of heat shock protein 90: Investigation by docking simulation and experimental validation
    • Abu Sheikha G, Al-Sha'er MA, Taha MO (2011) Some sulfonamide drugs inhibit ATPase activity of heat shock protein 90: investigation by docking simulation and experimental validation. J Enzym Inhibit Med Chem 26:603-609.
    • (2011) J Enzym Inhibit Med Chem , vol.26 , pp. 603-609
    • Abu, S.G.1    Al-Sha'er, M.A.2    Taha, M.O.3
  • 87
    • 77957221382 scopus 로고    scopus 로고
    • Elaborate ligand-based modeling reveal new nanomolar heat shock protein 90a inhibitors
    • Al-Sha'er MA, Taha MO (2010) Elaborate ligand-based modeling reveal new nanomolar heat shock protein 90a inhibitors. J Chem Inf Model 50:1706-1723.
    • (2010) J Chem Inf Model , vol.50 , pp. 1706-1723
    • Al-Sha'er, M.A.1    Taha, M.O.2
  • 88
    • 56049116069 scopus 로고    scopus 로고
    • Discovery of DPP IV inhibitors by pharmacophore modeling and QSAR analysis followed by in silico screening
    • Al-masri IM, Mohammad MK, Taha MO (2008) Discovery of DPP IV inhibitors by pharmacophore modeling and QSAR analysis followed by in silico screening. Chem Med Chem 3:1763-1779.
    • (2008) Chem Med Chem , vol.3 , pp. 1763-1779
    • Al-Masri, I.M.1    Mohammad, M.K.2    Taha, M.O.3
  • 89
    • 77955557891 scopus 로고    scopus 로고
    • Discovery of novel CDK1 inhibitors by combining pharmacophore modeling, QSAR analysis and in silico screening followed by in vitro bioassay
    • Al-Sha'er MA, Taha MO (2010) Discovery of novel CDK1 inhibitors by combining pharmacophore modeling, QSAR analysis and in silico screening followed by in vitro bioassay. Eur J Med Chem 45:4316-4330.
    • (2010) Eur J Med Chem , vol.45 , pp. 4316-4330
    • Al-Sha'er, M.A.1    Taha, M.O.2
  • 90
    • 13844312649 scopus 로고    scopus 로고
    • ZINC-A free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK (2005) ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 45:177-182.
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 92
    • 0346996357 scopus 로고    scopus 로고
    • Improving structure-based virtual screening by multivariate analysis of scoring data
    • Jacobsson M, Liden P, Stjernschantz E, Bostroem H, Norinder U (2003) Improving structure-based virtual screening by multivariate analysis of scoring data. J Med Chem 46:5781-5789.
    • (2003) J Med Chem , vol.46 , pp. 5781-5789
    • Jacobsson, M.1    Liden, P.2    Stjernschantz, E.3    Bostroem, H.4    Norinder, U.5
  • 93
    • 17144385534 scopus 로고    scopus 로고
    • Virtual screening workflow development guided by the "receiver operating characteristic" curve approach
    • Application to high-throughput docking on metabotropic glutamate receptor subtype
    • Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HO (2005) Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype. J Med Chem 48:2534-2547.
    • (2005) J Med Chem , vol.48 , pp. 2534-2547
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.P.4    Bertrand, H.O.5
  • 94
    • 13244266921 scopus 로고    scopus 로고
    • Lead- and drug-like compounds: The rule-offive revolution
    • Lipinski CA (2004) Lead- and drug-like compounds: the rule-offive revolution. Drug Discov Today Technol 1:337-341.
    • (2004) Drug Discov Today Technol , vol.1 , pp. 337-341
    • Lipinski, C.A.1


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