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Volumn 28, Issue 14, 2012, Pages 1845-1850

A holistic in silico approach to predict functional sites in protein structures

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN; RNA;

EID: 84864151560     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts269     Document Type: Article
Times cited : (31)

References (36)
  • 1
    • 0035800599 scopus 로고    scopus 로고
    • Structure-based analysis of protein-RNA interactions using the program ENTANGLE
    • Allers, J. and Shamoo, Y. (2001) Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol., 311, 75-86.
    • (2001) J. Mol. Biol. , vol.311 , pp. 75-86
    • Allers, J.1    Shamoo, Y.2
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S. F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389
    • Altschul, S.F.1
  • 3
    • 0030381077 scopus 로고    scopus 로고
    • The Quickhull algorithm for convex hulls
    • Barber, C. B. et al. (1996) The Quickhull algorithm for convex hulls. ACM Trans. Mathematical Softw., 22, 469-483.
    • (1996) ACM Trans. Mathematical Softw. , vol.22 , pp. 469-483
    • Barber, C.B.1
  • 4
    • 33846900499 scopus 로고    scopus 로고
    • Structure Based Prediction of Binding Residues on DNAbinding Proteins
    • Bhardwaj, N. et al. (2005). Structure Based Prediction of Binding Residues on DNAbinding Proteins. Conf Proc IEEE Eng Med Biol Soc, 3, 2611-2614.
    • (2005) Conf Proc IEEE Eng Med Biol Soc , vol.3 , pp. 2611-2614
    • Bhardwaj, N.1
  • 5
    • 71049146392 scopus 로고    scopus 로고
    • SitesIdentify: a protein functional site prediction tool
    • Bray, T. et al. (2009) SitesIdentify: a protein functional site prediction tool. BMC Bioinformatics, 10, 379.
    • (2009) BMC Bioinformatics , vol.10 , pp. 379
    • Bray, T.1
  • 7
    • 41949120229 scopus 로고    scopus 로고
    • Functional site prediction selects correct protein models
    • Chelliah, V. and Taylor, W. R. (2008) Functional site prediction selects correct protein models, BMC Bioinformatics, 9 (Suppl. 1), S13.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 1
    • Chelliah, V.1    Taylor, W.R.2
  • 8
    • 57649181721 scopus 로고    scopus 로고
    • Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
    • Cheng, C. W. et al. (2008) Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics, 9 (Suppl. 12), S6.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 12
    • Cheng, C.W.1
  • 9
    • 33646044395 scopus 로고    scopus 로고
    • WHISCY: what information does surface conservation yield? Application to data-driven docking
    • de Vries, S. J. et al. (2006) WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins, 63, 479-489.
    • (2006) Proteins , vol.63 , pp. 479-489
    • de Vries, S.J.1
  • 10
    • 0029071516 scopus 로고
    • Protein-RNA recognition
    • Draper, D. E. (1995) Protein-RNA recognition. Ann. Rev. Biochem., 64, 593-620.
    • (1995) Ann. Rev. Biochem. , vol.64 , pp. 593-620
    • Draper, D.E.1
  • 11
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • Glaser, F. et al. (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins, 43, 89.
    • (2001) Proteins , vol.43 , pp. 89
    • Glaser, F.1
  • 12
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    • Guerois, R. et al. (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol., 320, 369-387.
    • (2002) J. Mol. Biol. , vol.320 , pp. 369-387
    • Guerois, R.1
  • 13
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • Hwang, H. et al. (2010) Protein-protein docking benchmark version 4. 0. Proteins, 78, 3111-3114.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1
  • 14
    • 34547600100 scopus 로고    scopus 로고
    • siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins
    • Innis, C. A. (2007) siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. Nucleic Acids Res., 35, W489-W494.
    • (2007) Nucleic Acids Res , vol.35
    • Innis, C.A.1
  • 15
    • 0033574510 scopus 로고    scopus 로고
    • Protein-DNA interactions: a structural analysis
    • Jones, S. et al. (1999) Protein-DNA interactions: a structural analysis. J. Mol. Biol., 287, 877-896.
    • (1999) J. Mol. Biol. , vol.287 , pp. 877-896
    • Jones, S.1
  • 16
    • 0035865891 scopus 로고    scopus 로고
    • Protein-RNA interactions: a structural analysis
    • Jones, S. et al. (2001) Protein-RNA interactions: a structural analysis. Nucleic Acids Res., 29, 943-954.
    • (2001) Nucleic Acids Res , vol.29 , pp. 943-954
    • Jones, S.1
  • 17
    • 0035853280 scopus 로고    scopus 로고
    • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
    • Landgraf, R. et al. (2001) Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol., 307, 1487.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1487
    • Landgraf, R.1
  • 18
    • 0345040873 scopus 로고    scopus 로고
    • Classification and Regression by random Forest
    • Liaw, A. andWiener, M. (2002) Classification and Regression by random Forest. R News, 2, 18-22.
    • (2002) R News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 19
    • 77954185426 scopus 로고    scopus 로고
    • Prediction of protein-RNA binding sites by a random forest method with combined features
    • Liu, Z. P. et al. (2010) Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, 26, 1616-1622.
    • (2010) Bioinformatics , vol.26 , pp. 1616-1622
    • Liu, Z.P.1
  • 20
    • 75849126506 scopus 로고    scopus 로고
    • The structural basis of peptide-protein binding strategies
    • London, N. et al. (2010) The structural basis of peptide-protein binding strategies. Structure, 18, 188-199.
    • (2010) Structure , vol.18 , pp. 188-199
    • London, N.1
  • 21
    • 0033647653 scopus 로고    scopus 로고
    • An overview of the structures of protein-DNA complexes
    • reviews001. 001-reviews001. 037
    • Luscombe, N. M. et al. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, reviews001. 001-reviews001. 037.
    • (2000) Genome Biol , vol.1
    • Luscombe, N.M.1
  • 22
    • 71749114914 scopus 로고    scopus 로고
    • Exploiting structural and topological information to improve prediction of RNA-protein binding sites
    • Maetschke, S. R. and Yuan, Z. (2009) Exploiting structural and topological information to improve prediction of RNA-protein binding sites. BMC Bioinformatics, 10, 341.
    • (2009) BMC Bioinformatics , vol.10 , pp. 341
    • Maetschke, S.R.1    Yuan, Z.2
  • 23
    • 43249104982 scopus 로고    scopus 로고
    • PSAIA - protein structure and interaction analyzer
    • Mihel, J. et al. (2008) PSAIA - protein structure and interaction analyzer. BMC Struct. Biol., 8, 21.
    • (2008) BMC Struct. Biol. , vol.8 , pp. 21
    • Mihel, J.1
  • 24
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536
    • Murzin, A.G.1
  • 25
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: calculation of positional conservation in a protein sequence alignment
    • Pei, J. and Grishin, N. V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 26
    • 49549083915 scopus 로고    scopus 로고
    • Peptide-mediated interactions in biological systems: new discoveries and applications
    • Petsalaki, E. and Russell, R. B. (2008) Peptide-mediated interactions in biological systems: new discoveries and applications. Curr. Opin. Biotechnol., 19, 344-350.
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 344-350
    • Petsalaki, E.1    Russell, R.B.2
  • 27
    • 63549128280 scopus 로고    scopus 로고
    • Accurate prediction of peptide binding sites on protein surfaces
    • Petsalaki, E. et al. (2009)Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput. Biol., 5, e1000335.
    • (2009) PLoS Comput. Biol. , vol.5
    • Petsalaki, E.1
  • 28
    • 34248232474 scopus 로고    scopus 로고
    • HotPatch: a statistical approach to finding biologically relevant features on protein surfaces
    • Pettit, F. K. et al. (2007) HotPatch: a statistical approach to finding biologically relevant features on protein surfaces. J. Mol. Biol., 369, 863-879.
    • (2007) J. Mol. Biol. , vol.369 , pp. 863-879
    • Pettit, F.K.1
  • 29
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K. D. et al. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1
  • 30
    • 80052028418 scopus 로고    scopus 로고
    • Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams
    • Segura, J. et al. (2011) Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. BMC Bioinformatics, 12, 352.
    • (2011) BMC Bioinformatics , vol.12 , pp. 352
    • Segura, J.1
  • 31
    • 59149087824 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites in sequences and 3D structures by random forests
    • Sikic, M. et al. (2009) Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput. Biol., 5, e1000278.
    • (2009) PLoS Comput. Biol. , vol.5
    • Sikic, M.1
  • 32
    • 34547560560 scopus 로고    scopus 로고
    • RNABindR: a server for analyzing and predicting RNAbinding sites in proteins
    • Terribilini, M. et al. (2007) RNABindR: a server for analyzing and predicting RNAbinding sites in proteins. Nucleic Acids Res., 35, W578-W584.
    • (2007) Nucleic Acids Res , vol.35
    • Terribilini, M.1
  • 33
    • 33846803179 scopus 로고    scopus 로고
    • DISPLAR: an accurate method for predicting DNAbinding sites on protein surfaces
    • Tjong, H. and Zhou, H. X. (2007) DISPLAR: an accurate method for predicting DNAbinding sites on protein surfaces. Nucleic Acids Res., 35, 1465-1477.
    • (2007) Nucleic Acids Res , vol.35 , pp. 1465-1477
    • Tjong, H.1    Zhou, H.X.2
  • 34
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of proteinprotein interactions
    • von Mering, C. et al. (2002) Comparative assessment of large-scale data sets of proteinprotein interactions. Nature, 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1
  • 35
    • 0028922586 scopus 로고
    • LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A. C. et al. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127.
    • (1995) Protein Eng , vol.8 , pp. 127
    • Wallace, A.C.1
  • 36
    • 78650777069 scopus 로고    scopus 로고
    • An accurate feature-based method for identifying DNA-binding residues on protein surfaces
    • Xiong, Y. et al. (2011) An accurate feature-based method for identifying DNA-binding residues on protein surfaces. Proteins, 79, 509-517.
    • (2011) Proteins , vol.79 , pp. 509-517
    • Xiong, Y.1


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