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Volumn 35, Issue SUPPL.2, 2007, Pages

ProMateus-an open research approach to protein-binding sites analysis

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN;

EID: 34547579399     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm301     Document Type: Article
Times cited : (20)

References (27)
  • 1
    • 1542400269 scopus 로고    scopus 로고
    • Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
    • Ahmad, S., Gromiha, M.M. and Sarai, A. (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
    • (2004) Bioinformatics , vol.20 , pp. 477-486
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 2
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • Bradford, J.R. and Westhead, D.R. (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics, 21, 1487-1494.
    • (2005) Bioinformatics , vol.21 , pp. 1487-1494
    • Bradford, J.R.1    Westhead, D.R.2
  • 3
    • 33646044395 scopus 로고    scopus 로고
    • WHISCY: What information does surface conservation yield? Application to data-driven docking
    • de Vries, S.J., van Dijk, A.D. and Bonvin, A.M. (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    Van Dijk, A.D.2    Bonvin, A.M.3
  • 4
    • 23144448512 scopus 로고    scopus 로고
    • ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures
    • Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. and Ben-Tal, N. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, W299-W302.
    • (2005) Nucleic Acids Res. , vol.33
    • Landau, M.1    Mayrose, I.2    Rosenberg, Y.3    Glaser, F.4    Martz, E.5    Pupko, T.6    Ben-Tal, N.7
  • 5
    • 17444373556 scopus 로고    scopus 로고
    • PreDs: A server for predicting dsDNA-binding site on protein molecular surfaces
    • Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces. Bioinformatics, 21, 1721-1723.
    • (2005) Bioinformatics , vol.21 , pp. 1721-1723
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 6
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur, R.P., Chakrabarti, P., Rodier, F. and Janin, J. (2004) A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol., 336, 943-955.
    • (2004) J. Mol. Biol. , vol.336 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 7
    • 23044487169 scopus 로고    scopus 로고
    • Statistical analysis and prediction of protein-protein interfaces
    • Bordner, A.J. and Abagyan, R. (2005) Statistical analysis and prediction of protein-protein interfaces. Proteins, 60, 353-366.
    • (2005) Proteins , vol.60 , pp. 353-366
    • Bordner, A.J.1    Abagyan, R.2
  • 8
    • 2942553723 scopus 로고    scopus 로고
    • Protein-protein interactions; Coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking
    • Halperin, I., Wolfso, H. and Nussinov, R. (2004) Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure, 12, 1027-1038.
    • (2004) Structure , vol.12 , pp. 1027-1038
    • Halperin, I.1    Wolfso, H.2    Nussinov, R.3
  • 9
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • Liang, S., Zhang, C., Liu, S. and Zhou, Y. (2006) Protein binding site prediction using an empirical scoring function. Nucleic Acids Res., 34, 3698-3707.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4
  • 10
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren, I.M. and Thornton, J.M. (2003) Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol., 325, 991-1018.
    • (2003) J. Mol. Biol. , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 11
    • 30644470508 scopus 로고    scopus 로고
    • Predicting protein interaction sites from residue spatial sequence profile and evolution rate
    • Wang, B., Chen, P., Huang, D.S., Li, J.J., Lok, T.M. and Lyu, M.R. (2006) Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett., 580, 380-384.
    • (2006) FEBS Lett. , vol.580 , pp. 380-384
    • Wang, B.1    Chen, P.2    Huang, D.S.3    Li, J.J.4    Lok, T.M.5    Lyu, M.R.6
  • 12
    • 0346733329 scopus 로고    scopus 로고
    • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    • Caffrey, D.R., Somaroo, S., Hughes, J.D., Mintseris, J. and Huang, E.S. (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci., 13, 190-202.
    • (2004) Protein Sci. , vol.13 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5
  • 13
    • 27344440132 scopus 로고    scopus 로고
    • Conservation and relative importance of residues across protein-protein interfaces
    • Guharoy, M. and Chakrabarti, P. (2005) Conservation and relative importance of residues across protein-protein interfaces. Proc. Natl Acad. Sci. USA, 102, 15447-15452.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15447-15452
    • Guharoy, M.1    Chakrabarti, P.2
  • 14
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: A structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth, H., Raz, R. and Schreiber, G. (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol., 338, 181-199.
    • (2004) J. Mol. Biol. , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 15
    • 22444434743 scopus 로고    scopus 로고
    • Looking at enzymes from the inside out: The proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces
    • Ben-Shimon, A. and Eisenstein, M. (2005) Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. J. Mol. Biol., 351, 309-326.
    • (2005) J. Mol. Biol. , vol.351 , pp. 309-326
    • Ben-Shimon, A.1    Eisenstein, M.2
  • 16
    • 21244506296 scopus 로고    scopus 로고
    • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
    • Haliloglu, T., Keskin, O., Ma, B. and Nussinov, R. (2005) How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys. J., 88, 1552-1559.
    • (2005) Biophys. J. , vol.88 , pp. 1552-1559
    • Haliloglu, T.1    Keskin, O.2    Ma, B.3    Nussinov, R.4
  • 17
    • 0042386412 scopus 로고    scopus 로고
    • Protein-DNA Interactions: The story so far and a new method for prediction
    • Jones, S. and Thornton, J.M. (2003) Protein-DNA Interactions: the story so far and a new method for prediction. Comp. Funct. Genomics, 4, 428-431.
    • (2003) Comp. Funct. Genomics , vol.4 , pp. 428-431
    • Jones, S.1    Thornton, J.M.2
  • 18
    • 2542557409 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
    • Tsuchiya, Y., Kinoshita, K. and Nakamura, H. (2004) Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 55, 885-894.
    • (2004) Proteins , vol.55 , pp. 885-894
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 19
    • 0346258292 scopus 로고    scopus 로고
    • Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
    • Jones, S., Shanahan, H.P., Berman, H.M. and Thornton, J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 7189-7198
    • Jones, S.1    Shanahan, H.P.2    Berman, H.M.3    Thornton, J.M.4
  • 21
    • 0033605858 scopus 로고    scopus 로고
    • Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction
    • Selzer, T. and Schreiber, G. (1999) Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction. J. Mol. Biol., 287, 409-419.
    • (1999) J. Mol. Biol. , vol.287 , pp. 409-419
    • Selzer, T.1    Schreiber, G.2
  • 23
    • 0029109468 scopus 로고
    • Protein-protein interactions: A review of protein dimer structures
    • Jones, S. and Thornton, J.M. (1995) Protein-protein interactions: a review of protein dimer structures. Prog. Biophys. Mol. Biol., 63, 31-65.
    • (1995) Prog. Biophys. Mol. Biol. , vol.63 , pp. 31-65
    • Jones, S.1    Thornton, J.M.2
  • 24
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge, A., Bartlett, G.J. and Thornton, J.M. (2003) Using a neural network and spatial clustering to predict the location of active sites in enzymes. J. Mol. Biol., 330, 719-734.
    • (2003) J. Mol. Biol. , vol.330 , pp. 719-734
    • Gutteridge, A.1    Bartlett, G.J.2    Thornton, J.M.3
  • 25
    • 33646122452 scopus 로고    scopus 로고
    • An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements
    • Hoskins, J., Lovell, S. and Blundell, T.L. (2006) An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements. Protein Sci., 15, 1017-1029.
    • (2006) Protein Sci. , vol.15 , pp. 1017-1029
    • Hoskins, J.1    Lovell, S.2    Blundell, T.L.3
  • 26
    • 33846684074 scopus 로고    scopus 로고
    • Rediscovering secondary structures as network motifs-an unsupervised learning approach
    • Raveh, B., Rahat, O., Basri, R. and Schreiber, G. (2007) Rediscovering secondary structures as network motifs-an unsupervised learning approach. Bioinformatics., 23, e163-9
    • (2007) Bioinformatics. , vol.23
    • Raveh, B.1    Rahat, O.2    Basri, R.3    Schreiber, G.4
  • 27
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF-a program to identify and analyze structural motifs in proteins
    • Hutchinson, E.G. and Thornton, J.M. (1996) PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci., 5, 212-220.
    • (1996) Protein Sci. , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.