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Volumn 10, Issue 7, 2014, Pages

Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CRYSTAL STRUCTURE; MAMMALS;

EID: 84905454868     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003741     Document Type: Article
Times cited : (29)

References (38)
  • 1
    • 33645887230 scopus 로고    scopus 로고
    • Critical review of the role of HTS in drug discovery
    • Macarron R, (2006) Critical review of the role of HTS in drug discovery. Drug Discov Today 11: 277-279.
    • (2006) Drug Discov Today , vol.11 , pp. 277-279
    • Macarron, R.1
  • 3
    • 54849423239 scopus 로고    scopus 로고
    • Predicting selectivity and druggability in drug discovery
    • Cheng AC, (2008) Predicting selectivity and druggability in drug discovery. Annual Reports Comp Chem 4: 23-37.
    • (2008) Annual Reports Comp Chem , vol.4 , pp. 23-37
    • Cheng, A.C.1
  • 4
    • 33846155913 scopus 로고    scopus 로고
    • Structure-based maximal affinity model predicts small molecule druggability
    • Cheng AC, Coleman RG, Smyth KT, Cao Q, Soulard P, et al. (2007) Structure-based maximal affinity model predicts small molecule druggability. Nature Biotech 25: 71-75.
    • (2007) Nature Biotech , vol.25 , pp. 71-75
    • Cheng, A.C.1    Coleman, R.G.2    Smyth, K.T.3    Cao, Q.4    Soulard, P.5
  • 5
  • 6
    • 79960985571 scopus 로고    scopus 로고
    • Structure-based druggability assessment-identifying suitable targets for small molecule therapeutics
    • Fauman EB, Rai BK, Huang ES, (2011) Structure-based druggability assessment-identifying suitable targets for small molecule therapeutics. Curr Opin Chem Biol 15: 463-468.
    • (2011) Curr Opin Chem Biol , vol.15 , pp. 463-468
    • Fauman, E.B.1    Rai, B.K.2    Huang, E.S.3
  • 7
    • 78649523910 scopus 로고    scopus 로고
    • Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank
    • Sheridan RP, Maiorov VN, Holloway MK, Cornell WD, Gao YD, (2010) Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank. J Chem Inf Model 50: 2029-2040.
    • (2010) J Chem Inf Model , vol.50 , pp. 2029-2040
    • Sheridan, R.P.1    Maiorov, V.N.2    Holloway, M.K.3    Cornell, W.D.4    Gao, Y.D.5
  • 8
    • 65449159794 scopus 로고    scopus 로고
    • Binding site detection and druggability index from first principles
    • Seco J, Luque FJ, Barril X, (2009) Binding site detection and druggability index from first principles. J Med Chem 52: 2363-2371.
    • (2009) J Med Chem , vol.52 , pp. 2363-2371
    • Seco, J.1    Luque, F.J.2    Barril, X.3
  • 9
    • 84856776282 scopus 로고    scopus 로고
    • Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
    • Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, et al. (2012) Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization. Proteins 80: 871-883.
    • (2012) Proteins , vol.80 , pp. 871-883
    • Beuming, T.1    Che, Y.2    Abel, R.3    Kim, B.4    Shanmugasundaram, V.5
  • 10
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • Wells JA, McClendon CL, (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450: 1001-1009.
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 11
    • 34547583152 scopus 로고    scopus 로고
    • Transient pockets on protein surfaces involved in protein-protein interaction
    • Eyrisch S, Helms V, (2007) Transient pockets on protein surfaces involved in protein-protein interaction. J Med Chem 50: 3457-3464.
    • (2007) J Med Chem , vol.50 , pp. 3457-3464
    • Eyrisch, S.1    Helms, V.2
  • 12
    • 84876546810 scopus 로고    scopus 로고
    • 2P2Idb: A Structural Database Dedicated to Orthosteric Modulation of Protein-Protein Interactions
    • Basse MJ, Betzi S, Bourgeas R, Bouzidi S, Chetrit B, et al. (2013) 2P2Idb: A Structural Database Dedicated to Orthosteric Modulation of Protein-Protein Interactions. Nucleic Acid Research 41: D824-827.
    • (2013) Nucleic Acid Research , vol.41
    • Basse, M.J.1    Betzi, S.2    Bourgeas, R.3    Bouzidi, S.4    Chetrit, B.5
  • 13
    • 65249117514 scopus 로고    scopus 로고
    • Identifying and characterizing binding sites and assessing druggability
    • Halgren TA, (2009) Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 49: 377-389.
    • (2009) J Chem Inf Model , vol.49 , pp. 377-389
    • Halgren, T.A.1
  • 14
    • 84863052839 scopus 로고    scopus 로고
    • Fragment based drug discovery: practical implementation based on 19F NMR spectroscopy
    • Jordan JB, Poppe L, Xia X, Cheng AC, Sun Y, et al. (2012) Fragment based drug discovery: practical implementation based on 19F NMR spectroscopy. J Med Chem 55: 678-687.
    • (2012) J Med Chem , vol.55 , pp. 678-687
    • Jordan, J.B.1    Poppe, L.2    Xia, X.3    Cheng, A.C.4    Sun, Y.5
  • 15
    • 84880625796 scopus 로고    scopus 로고
    • Structure guided design of a series of sphingosine kinase (SphK) inhibitors
    • Gustin DJ, Li Y, Brown ML, Min X, Schmitt MJ, et al. (2013) Structure guided design of a series of sphingosine kinase (SphK) inhibitors. Bioorg Med Chem Lett 23: 4608-4616.
    • (2013) Bioorg Med Chem Lett , vol.23 , pp. 4608-4616
    • Gustin, D.J.1    Li, Y.2    Brown, M.L.3    Min, X.4    Schmitt, M.J.5
  • 16
    • 31544450787 scopus 로고    scopus 로고
    • Novel procedure for modeling ligand/receptor induced fit effects
    • Sherman W, Day T, Jacobson MP, Friesner RA, Farid R, (2006) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49: 534-553.
    • (2006) J Med Chem , vol.49 , pp. 534-553
    • Sherman, W.1    Day, T.2    Jacobson, M.P.3    Friesner, R.A.4    Farid, R.5
  • 17
    • 77956308900 scopus 로고    scopus 로고
    • Binding-site assessment by virtual fragment screening
    • Huang N, Jacobson MP, (2010) Binding-site assessment by virtual fragment screening. PLoS One 5: e10109.
    • (2010) PLoS One , vol.5
    • Huang, N.1    Jacobson, M.P.2
  • 18
    • 80051966197 scopus 로고    scopus 로고
    • Structural conservation of druggable hot spots in protein-protein interfaces
    • Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, et al. (2011) Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci USA 108: 13528-13533.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 13528-13533
    • Kozakov, D.1    Hall, D.R.2    Chuang, G.Y.3    Cencic, R.4    Brenke, R.5
  • 19
    • 84886389108 scopus 로고    scopus 로고
    • FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
    • Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D, (2013) FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics 29: 1218-1219.
    • (2013) Bioinformatics , vol.29 , pp. 1218-1219
    • Grove, L.E.1    Hall, D.R.2    Beglov, D.3    Vajda, S.4    Kozakov, D.5
  • 20
    • 84863661333 scopus 로고    scopus 로고
    • Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules
    • Bakan A, Nevins N, Lakdawala AS, Bahar I, (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules. J Chem Theory Comput 8: 2435-2447.
    • (2012) J Chem Theory Comput , vol.8 , pp. 2435-2447
    • Bakan, A.1    Nevins, N.2    Lakdawala, A.S.3    Bahar, I.4
  • 21
    • 33746076877 scopus 로고    scopus 로고
    • Effects of conformational dynamics on predicted protein druggability
    • Brown SP, Hajduk PJ, (2006) Effects of conformational dynamics on predicted protein druggability. ChemMedChem 1: 70-72.
    • (2006) ChemMedChem , vol.1 , pp. 70-72
    • Brown, S.P.1    Hajduk, P.J.2
  • 23
    • 82255164267 scopus 로고    scopus 로고
    • MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
    • Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X, (2011) MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories. Bioinformatics 27: 3276-3285.
    • (2011) Bioinformatics , vol.27 , pp. 3276-3285
    • Schmidtke, P.1    Bidon-Chanal, A.2    Luque, F.J.3    Barril, X.4
  • 24
    • 84855955506 scopus 로고    scopus 로고
    • A molecular dynamics ensemble-based approach for the mapping of druggable binding sites
    • Ivetac A, McCammon JA, (2012) A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods Mol Biol. 819: 3-12.
    • (2012) Methods Mol Biol , vol.819 , pp. 3-12
    • Ivetac, A.1    McCammon, J.A.2
  • 25
    • 78651402672 scopus 로고    scopus 로고
    • Full protein flexibility is essential for proper hot-spot mapping
    • Lexa KW, Carlson HA, (2011) Full protein flexibility is essential for proper hot-spot mapping. J Am Chem Soc 133: 200-202.
    • (2011) J Am Chem Soc , vol.133 , pp. 200-202
    • Lexa, K.W.1    Carlson, H.A.2
  • 29
    • 34548047900 scopus 로고    scopus 로고
    • Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family
    • Lee EF, Czabotar PE, Smith BJ, Deshayes K, Zobel K, et al. (2007) Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family. Cell Death Differ 14: 1711-1713.
    • (2007) Cell Death Differ , vol.14 , pp. 1711-1713
    • Lee, E.F.1    Czabotar, P.E.2    Smith, B.J.3    Deshayes, K.4    Zobel, K.5
  • 31
    • 84861015413 scopus 로고    scopus 로고
    • InterEvol database: Exploring the structure and evolution of protein complex interfaces
    • Faure G, Andreani J, Guerois R, (2012) InterEvol database: Exploring the structure and evolution of protein complex interfaces. Nucleic Acids Res 40: D847-56 (Used July 2012 release from http://biodev.cea.fr/interevol/, downloaded May 26, 2013.).
    • (2012) Nucleic Acids Res , vol.40
    • Faure, G.1    Andreani, J.2    Guerois, R.3
  • 32
    • 33845806987 scopus 로고    scopus 로고
    • Structure-based identification of small molecule binding sites using a free energy model
    • Coleman RG, Salzberg AC, Cheng AC, (2006) Structure-based identification of small molecule binding sites using a free energy model. J Chem Inf Model 46: 2631-2637.
    • (2006) J Chem Inf Model , vol.46 , pp. 2631-2637
    • Coleman, R.G.1    Salzberg, A.C.2    Cheng, A.C.3
  • 33
    • 84875984520 scopus 로고    scopus 로고
    • Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface
    • Johnson DK, Karanicolas J, (2013) Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol 9: e1002951.
    • (2013) PLoS Comput Biol , vol.9
    • Johnson, D.K.1    Karanicolas, J.2
  • 34
    • 84856370676 scopus 로고    scopus 로고
    • Pocketome: an encyclopedia of small-molecule binding sites in 4D
    • Kufareva I, Ilatovskiy AV, Abagyan R, (2012) Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res 40: D535-40.
    • (2012) Nucleic Acids Res , vol.40
    • Kufareva, I.1    Ilatovskiy, A.V.2    Abagyan, R.3
  • 36
    • 28444469788 scopus 로고    scopus 로고
    • Mapping PDB chains to UniProtKB entries
    • Downloaded March 6, 2013 update
    • Martin AC (2005) Mapping PDB chains to UniProtKB entries. Bioinformatics 21: 4297-4301. Downloaded March 6, 2013 update.
    • (2005) Bioinformatics , vol.21 , pp. 4297-4301
    • Martin, A.C.1


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