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Volumn 31, Issue 5, 2015, Pages 707-713

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 84928989421     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu724     Document Type: Article
Times cited : (49)

References (32)
  • 1
    • 2442677781 scopus 로고    scopus 로고
    • Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
    • Arakaki, A.K. et al. (2004) Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics, 20, 1087-1096.
    • (2004) Bioinformatics , vol.20 , pp. 1087-1096
    • Arakaki, A.K.1
  • 2
    • 67650912101 scopus 로고    scopus 로고
    • FINDSITE: A threading-based approach to ligand homology modeling
    • Brylinski, M. and Skolnick, J. (2009) FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput. Biol., 5, e1000405.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000405
    • Brylinski, M.1    Skolnick, J.2
  • 4
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • Capra, J.A. et al. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol., 5, e1000585.
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000585
    • Capra, J.A.1
  • 5
    • 77953587057 scopus 로고    scopus 로고
    • Real-time ligand binding pocket database search using local surface descriptors
    • Chikhi, R. et al. (2010) Real-time ligand binding pocket database search using local surface descriptors. Proteins, 78, 2007-2028.
    • (2010) Proteins , vol.78 , pp. 2007-2028
    • Chikhi, R.1
  • 6
    • 73349097886 scopus 로고    scopus 로고
    • Rapid comparison of protein binding site surfaces with property encoded shape distributions
    • Das, S. et al. (2009) Rapid comparison of protein binding site surfaces with property encoded shape distributions. J. Chem. Inform. Model., 49, 2863-2872.
    • (2009) J. Chem. Inform. Model. , vol.49 , pp. 2863-2872
    • Das, S.1
  • 7
    • 0035882572 scopus 로고    scopus 로고
    • Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins
    • Denessiouk, K.A. et al. (2001) Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins, 44, 282-291.
    • (2001) Proteins , vol.44 , pp. 282-291
    • Denessiouk, K.A.1
  • 8
    • 84874754249 scopus 로고    scopus 로고
    • APoc: Large-scale identification of similar protein pockets
    • Gao, M. and Skolnick, J. (2013) APoc: large-scale identification of similar protein pockets. Bioinformatics, 29, 597-604.
    • (2013) Bioinformatics , vol.29 , pp. 597-604
    • Gao, M.1    Skolnick, J.2
  • 9
    • 29444457054 scopus 로고    scopus 로고
    • Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships
    • Gold, N.D. and Jackson, R.M. (2006) Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J. Mol. Biol., 355, 1112-1124.
    • (2006) J. Mol. Biol. , vol.355 , pp. 1112-1124
    • Gold, N.D.1    Jackson, R.M.2
  • 10
    • 0141843591 scopus 로고    scopus 로고
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    • Hattori, M. et al. (2003) Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc., 125, 11853-11865.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 11853-11865
    • Hattori, M.1
  • 11
    • 84904823376 scopus 로고    scopus 로고
    • GalaxySite: Ligand-binding-site prediction by using molecular docking
    • Heo, L. et al. (2014) GalaxySite: ligand-binding-site prediction by using molecular docking. Nucleic Acids Res., 42, W210-W214.
    • (2014) Nucleic Acids Res. , vol.42 , pp. W210-W214
    • Heo, L.1
  • 12
    • 77950423796 scopus 로고    scopus 로고
    • A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: Application to ligand prediction
    • Hoffmann, B. et al. (2010) A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics, 11, 99.
    • (2010) BMC Bioinformatics , vol.11 , pp. 99
    • Hoffmann, B.1
  • 13
    • 84868573142 scopus 로고    scopus 로고
    • Finding protein targets for small biologically relevant lig-ands across fold space using inverse ligand binding predictions
    • Hu, G. et al. (2012) Finding protein targets for small biologically relevant lig-ands across fold space using inverse ligand binding predictions, Structure, 20, 1815-1822.
    • (2012) Structure , vol.20 , pp. 1815-1822
    • Hu, G.1
  • 14
    • 33947420139 scopus 로고    scopus 로고
    • Shape variation in protein binding pockets and their ligands
    • Kahraman, A. et al. (2007) Shape variation in protein binding pockets and their ligands. J. Mol. Biol., 368, 283-301.
    • (2007) J. Mol. Biol. , vol.368 , pp. 283-301
    • Kahraman, A.1
  • 15
    • 77951217659 scopus 로고    scopus 로고
    • Detection of multiscale pockets on protein surfaces using mathematical morphology
    • Kawabata, T. (2010) Detection of multiscale pockets on protein surfaces using mathematical morphology. Proteins, 78, 1195-1211.
    • (2010) Proteins , vol.78 , pp. 1195-1211
    • Kawabata, T.1
  • 16
    • 80052230202 scopus 로고    scopus 로고
    • Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking
    • Kihara, D. et al. (2011) Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. Curr. Protein Pept. Sci. 12, 520-530.
    • (2011) Curr. Protein Pept. Sci. , vol.12 , pp. 520-530
    • Kihara, D.1
  • 17
    • 14144254344 scopus 로고    scopus 로고
    • Identification of the ligand binding sites on the molecular surface of proteins
    • Kinoshita, K. and Nakamura, H. (2005) Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci., 14, 711.
    • (2005) Protein Sci. , vol.14 , pp. 711
    • Kinoshita, K.1    Nakamura, H.2
  • 18
    • 41149093109 scopus 로고    scopus 로고
    • Characterization of local geometry of protein surfaces with the visibility criterion
    • Li, B. et al. (2008) Characterization of local geometry of protein surfaces with the visibility criterion. Proteins, 71, 670-683.
    • (2008) Proteins , vol.71 , pp. 670-683
    • Li, B.1
  • 19
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang, J. et al. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884.
    • (1998) Protein Sci. , vol.7 , pp. 1884
    • Liang, J.1
  • 20
    • 79953237284 scopus 로고    scopus 로고
    • Energetics-based discovery of protein-ligand interactions on a proteomic scale
    • Liu, P.F. et al. (2011) Energetics-based discovery of protein-ligand interactions on a proteomic scale. J. Mol. Biol., 408, 147-162.
    • (2011) J. Mol. Biol. , vol.408 , pp. 147-162
    • Liu, P.F.1
  • 21
    • 0030297640 scopus 로고    scopus 로고
    • Protein recognition of adenylate: An example of a fuzzy recognition template
    • Moodie, S.L. et al. (1996) Protein recognition of adenylate: an example of a fuzzy recognition template. J. Mol. Biol., 263, 486-500.
    • (1996) J. Mol. Biol. , vol.263 , pp. 486-500
    • Moodie, S.L.1
  • 22
    • 19544389524 scopus 로고    scopus 로고
    • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    • Morris, R.J. et al. (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics, 21, 2347-2355.
    • (2005) Bioinformatics , vol.21 , pp. 2347-2355
    • Morris, R.J.1
  • 23
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
    • Nagano, N. et al. (2002) One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol., 321, 741-765.
    • (2002) J. Mol. Biol. , vol.321 , pp. 741-765
    • Nagano, N.1
  • 24
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter, C.T. et al. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res., 32, D129-D133.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D129-D133
    • Porter, C.T.1
  • 25
    • 78650986186 scopus 로고    scopus 로고
    • Binding ligand prediction for proteins using partial matching of local surface patches
    • Sael, L. and Kihara, D. (2010) Binding ligand prediction for proteins using partial matching of local surface patches. Int. J. Mol. Sci., 11, 5009-5026.
    • (2010) Int. J. Mol. Sci. , vol.11 , pp. 5009-5026
    • Sael, L.1    Kihara, D.2
  • 26
    • 84857794078 scopus 로고    scopus 로고
    • Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison
    • Sael, L. and Kihara, D. (2012) Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. Proteins, 80, 1177-1195.
    • (2012) Proteins , vol.80 , pp. 1177-1195
    • Sael, L.1    Kihara, D.2
  • 27
    • 33645465515 scopus 로고    scopus 로고
    • The multiple common point set problem and its application to molecule binding pattern detection
    • Shatsky, M. et al. (2006) The multiple common point set problem and its application to molecule binding pattern detection. J. Comput. Biol., 13, 407-428.
    • (2006) J. Comput. Biol. , vol.13 , pp. 407-428
    • Shatsky, M.1
  • 28
    • 61449173017 scopus 로고    scopus 로고
    • The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding
    • Wallach, I. and Lilien, R. (2009) The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. Bioinformatics, 25, 615-620.
    • (2009) Bioinformatics , vol.25 , pp. 615-620
    • Wallach, I.1    Lilien, R.2
  • 29
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • Xie, L. and Bourne, P.E. (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Nat. Acad. Sci. US A., 105, 5441-5446.
    • (2008) Proc. Nat. Acad. Sci. US A. , vol.105 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 30
    • 84863529885 scopus 로고    scopus 로고
    • Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
    • Xie, Z.R. and Hwang, M.J. (2012) Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles. Bioinformatics, 28, 1579-1585.
    • (2012) Bioinformatics , vol.28 , pp. 1579-1585
    • Xie, Z.R.1    Hwang, M.J.2
  • 31
    • 84885655034 scopus 로고    scopus 로고
    • Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
    • Yang, J. et al. (2013) Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29, 2588-2595.
    • (2013) Bioinformatics , vol.29 , pp. 2588-2595
    • Yang, J.1
  • 32
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang, Y. and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302
    • Zhang, Y.1    Skolnick, J.2


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