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Volumn 18, Issue 4, 2012, Pages 1285-1297

Application of information theory to feature selection in protein docking

Author keywords

Feature selection; Mutual information; Protein interaction; Protein interface; Structure analysis

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; INFORMATION SCIENCE; MOLECULAR DOCKING; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

EID: 84861228225     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1157-6     Document Type: Article
Times cited : (7)

References (41)
  • 2
    • 77957934896 scopus 로고    scopus 로고
    • Docking and scoring protein interactions: CAPRI 2009
    • Lensink MF, Wodak SJ (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins 78:3073-3084
    • (2010) Proteins , vol.78 , pp. 3073-3084
    • Lensink, M.F.1    Wodak, S.J.2
  • 3
    • 78149422216 scopus 로고    scopus 로고
    • Protein-protein docking tested in blind predictions: The CAPRI experiment
    • Janin J (2010) Protein-protein docking tested in blind predictions: the CAPRI experiment. Mol Biosyst 6:2351-2362
    • (2010) Mol Biosyst , vol.6 , pp. 2351-2362
    • Janin, J.1
  • 4
    • 77957960073 scopus 로고    scopus 로고
    • The targets of CAPRI rounds 13-19
    • Janin J (2010) The targets of CAPRI rounds 13-19. Proteins 78:3067-3072
    • (2010) Proteins , vol.78 , pp. 3067-3072
    • Janin, J.1
  • 5
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 89:2195-2199
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 6
    • 0026464639 scopus 로고
    • New algorithm to model protein- protein recognition based on surface complementarity. Applications to antibody-antigen docking
    • Walls PH, Sternberg MJ (1992) New algorithm to model protein- protein recognition based on surface complementarity. Applications to antibody-antigen docking. J Mol Biol 228:277-297
    • (1992) J Mol Biol , vol.228 , pp. 277-297
    • Walls, P.H.1    Sternberg, M.J.2
  • 8
    • 0030598347 scopus 로고    scopus 로고
    • Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
    • DOI 10.1006/jmbi.1996.0634
    • Meyer M, Wilson P, Schomburg D (1996) Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol 264:199-210 (Pubitemid 26400004)
    • (1996) Journal of Molecular Biology , vol.264 , Issue.1 , pp. 199-210
    • Meyer, M.1    Wilson, P.2    Schomburg, D.3
  • 9
    • 0030855390 scopus 로고    scopus 로고
    • ESCHER: A new docking procedure applied to the reconstruction of protein tertiary structure
    • DOI 10.1002/(SICI)1097-0134(199708)28:4<556::AID-PROT9>3.0.CO;2-7
    • Ausiello G, Cesareni G, Helmer-Citterich M (1997) Escher: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins 28:556-567 (Pubitemid 27328571)
    • (1997) Proteins: Structure, Function and Genetics , vol.28 , Issue.4 , pp. 556-567
    • Ausiello, G.1    Cesareni, G.2    Helmer-Citterich, M.3
  • 10
    • 0028575449 scopus 로고
    • Hydrophobic docking: A proposed enhancement to molecular recognition techniques
    • Vakser IA, Aflalo C (1994) Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 20:320-329
    • (1994) Proteins , vol.20 , pp. 320-329
    • Vakser, I.A.1    Aflalo, C.2
  • 11
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • DOI 10.1006/jmbi.1997.1203
    • Gabb HA, Jackson RM, Sternberg MJ (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272:106-120 (Pubitemid 27395541)
    • (1997) Journal of Molecular Biology , vol.272 , Issue.1 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 12
    • 0032515101 scopus 로고    scopus 로고
    • A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions
    • DOI 10.1006/jmbi.1998.2152
    • Robert CH, Janin J (1998) A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. J Mol Biol 283:1037-1047 (Pubitemid 28515332)
    • (1998) Journal of Molecular Biology , vol.283 , Issue.5 , pp. 1037-1047
    • Robert, C.H.1    Janin, J.2
  • 13
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • DOI 10.1002/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2- 4
    • Moont G, Gabb HA, Sternberg MJ (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35:364-373 (Pubitemid 29200974)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.3 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.E.3
  • 14
    • 1642534609 scopus 로고    scopus 로고
    • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
    • DOI 10.1110/ps.03348304
    • Zhang C, Liu S, Zhou H, Zhou Y (2004) An accurate, residuelevel, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 13:400-411 (Pubitemid 38124961)
    • (2004) Protein Science , vol.13 , Issue.2 , pp. 400-411
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 15
    • 79952132540 scopus 로고    scopus 로고
    • Scoring by intermolecular pairwise propensities of exposed residues (sipper): A new efficient potential for protein-protein docking
    • Pons C, Talavera D, de la Cruz X, Orozco M, Fernandez-Recio J (2011) Scoring by intermolecular pairwise propensities of exposed residues (sipper): a new efficient potential for protein-protein docking. J Chem Inf Model 51:370-377
    • (2011) J Chem Inf Model , vol.51 , pp. 370-377
    • Pons, C.1    Talavera, D.2    De La Cruz, X.3    Orozco, M.4    Fernandez-Recio, J.5
  • 17
    • 33750406198 scopus 로고    scopus 로고
    • Dockground resource for studying protein-protein interfaces
    • DOI 10.1093/bioinformatics/btl447
    • Douguet D, Chen HC, Tovchigrechko A, Vakser IA (2006) Dockground resource for studying protein-protein interfaces. Bioinformatics 22:2612-2618 (Pubitemid 44642599)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2612-2618
    • Douguet, D.1    Chen, H.-C.2    Tovchigrechko, A.3    Vakser, I.A.4
  • 18
    • 36749060694 scopus 로고    scopus 로고
    • Dockground system of databases for protein recognition studies: Unbound structures for docking
    • DOI 10.1002/prot.21714
    • Gao Y, Douguet D, Tovchigrechko A, Vakser IA (2007) Dockground system of databases for protein recognition studies: unbound structures for docking. Proteins 69:845-851 (Pubitemid 350210147)
    • (2007) Proteins: Structure, Function and Genetics , vol.69 , Issue.4 , pp. 845-851
    • Gao, Y.1    Douguet, D.2    Tovchigrechko, A.3    Vakser, I.A.4
  • 19
    • 55749085508 scopus 로고    scopus 로고
    • Dockground protein-protein docking decoy set
    • Liu S, Gao Y, Vakser IA (2008) Dockground protein-protein docking decoy set. Bioinformatics 24:2634-2635
    • (2008) Bioinformatics , vol.24 , pp. 2634-2635
    • Liu, S.1    Gao, Y.2    Vakser, I.A.3
  • 20
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 21
    • 77952283120 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using electrostatic desolvation profiles
    • Fiorucci S, Zacharias M (2010) Prediction of protein-protein interaction sites using electrostatic desolvation profiles. Biophys J 98:1921-1930
    • (2010) Biophys J , vol.98 , pp. 1921-1930
    • Fiorucci, S.1    Zacharias, M.2
  • 23
    • 26444568633 scopus 로고    scopus 로고
    • Statistical analysis of predominantly transient protein-protein interfaces
    • DOI 10.1002/prot.20593
    • Ansari S, Helms V (2005) Statistical analysis of predominantly transient protein-protein interfaces. Proteins 61:344-355 (Pubitemid 41429142)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.2 , pp. 344-355
    • Ansari, S.1    Helms, V.2
  • 24
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic
    • DOI 10.1006/jmbi.1996.0868
    • Melo F, Feytmans E (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267:207-222 (Pubitemid 27149749)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.1 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 25
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • DOI 10.1110/ps.25502
    • Melo F, Sanchez R, Sali A (2002) Statistical potentials for fold assessment. Protein Sci 11:430-448 (Pubitemid 34075806)
    • (2002) Protein Science , vol.11 , Issue.2 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 26
    • 35348936054 scopus 로고    scopus 로고
    • Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets
    • Launay G, Mendez R, Wodak S, Simonson T (2007) Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. BMC Bioinforma 8:270
    • (2007) BMC Bioinforma , vol.8 , pp. 270
    • Launay, G.1    Mendez, R.2    Wodak, S.3    Simonson, T.4
  • 27
    • 77957958670 scopus 로고    scopus 로고
    • Binding site prediction and improved scoring during flexible protein-protein docking with attract
    • Fiorucci S, Zacharias M (2010) Binding site prediction and improved scoring during flexible protein-protein docking with attract. Proteins 78:3131-3139
    • (2010) Proteins , vol.78 , pp. 3131-3139
    • Fiorucci, S.1    Zacharias, M.2
  • 28
    • 55249084667 scopus 로고    scopus 로고
    • Structure and function of salmonella sifa indicate that its interactions with skip, ssej, and rhoa family gtpases induce endosomal tubulation
    • Ohlson MB, Huang Z, Alto NM, Blanc MP, Dixon JE, Chai J, Miller SI (2008) Structure and function of salmonella sifa indicate that its interactions with skip, ssej, and rhoa family gtpases induce endosomal tubulation. Cell Host Microbe 4:434-446
    • (2008) Cell Host Microbe , vol.4 , pp. 434-446
    • Ohlson, M.B.1    Huang, Z.2    Alto, N.M.3    Blanc, M.P.4    Dixon, J.E.5    Chai, J.6    Miller, S.I.7
  • 30
    • 77957771797 scopus 로고    scopus 로고
    • Transient protein-protein interactions: Structural, functional, and network properties
    • Perkins JR, Diboun I, Dessailly BH, Lees JG, Orengo C (2010) Transient protein-protein interactions: structural, functional, and network properties. Structure 18:1233-1243
    • (2010) Structure , vol.18 , pp. 1233-1243
    • Perkins, J.R.1    Diboun, I.2    Dessailly, B.H.3    Lees, J.G.4    Orengo, C.5
  • 31
    • 77950867698 scopus 로고    scopus 로고
    • The subunit interfaces of weakly associated homodimeric proteins
    • Dey S, Pal A, Chakrabarti P, Janin J (2010) The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 398:146-160
    • (2010) J Mol Biol , vol.398 , pp. 146-160
    • Dey, S.1    Pal, A.2    Chakrabarti, P.3    Janin, J.4
  • 32
    • 33847307576 scopus 로고    scopus 로고
    • Information theory in living systems, methods, applications, and challenges
    • DOI 10.1007/s11538-006-9141-5
    • Gatenby RA, Frieden BR (2007) Information theory in living systems, methods, applications, and challenges. Bull Math Biol 69:635-657 (Pubitemid 46327271)
    • (2007) Bulletin of Mathematical Biology , vol.69 , Issue.2 , pp. 635-657
    • Gatenby, R.A.1    Frieden, B.R.2
  • 33
    • 40549129763 scopus 로고    scopus 로고
    • An analysis of information content present in protein-DNA interactions
    • Kauffman C, Karypis G (2008) An analysis of information content present in protein-DNA interactions. Pac Symp Biocomput:477-488
    • (2008) Pac Symp Biocomput , pp. 477-488
    • Kauffman, C.1    Karypis, G.2
  • 34
    • 35948961101 scopus 로고    scopus 로고
    • Predicting and annotating catalytic residues: An information theoretic approach
    • DOI 10.1089/cmb.2007.0042
    • Sterner B, Singh R, Berger B (2007) Predicting and annotating catalytic residues: an information theoretic approach. J Comput Biol 14:1058-1073 (Pubitemid 350073526)
    • (2007) Journal of Computational Biology , vol.14 , Issue.8 , pp. 1058-1073
    • Sterner, B.1    Singh, R.2    Berger, B.3
  • 35
    • 27644527039 scopus 로고    scopus 로고
    • Sequence variation in ligand binding sites in proteins
    • Magliery TJ, Regan L (2005) Sequence variation in ligand binding sites in proteins. BMC Bioinforma 6:240
    • (2005) BMC Bioinforma , vol.6 , pp. 240
    • Magliery, T.J.1    Regan, L.2
  • 36
    • 56449121765 scopus 로고    scopus 로고
    • Information theorybased scoring function for the structure-based prediction of protein-ligand binding affinity
    • Kulharia M, Goody RS, Jackson RM (2008) Information theorybased scoring function for the structure-based prediction of protein-ligand binding affinity. J Chem Inf Model 48:1990-1998
    • (2008) J Chem Inf Model , vol.48 , pp. 1990-1998
    • Kulharia, M.1    Goody, R.S.2    Jackson, R.M.3
  • 37
    • 78649493849 scopus 로고    scopus 로고
    • Identification of descriptors capturing compound class-specific features by mutual information analysis
    • Wassermann AM, Nisius B, Vogt M, Bajorath J (2010) Identification of descriptors capturing compound class-specific features by mutual information analysis. J Chem Inf Model 50:1935-1940
    • (2010) J Chem Inf Model , vol.50 , pp. 1935-1940
    • Wassermann, A.M.1    Nisius, B.2    Vogt, M.3    Bajorath, J.4
  • 39
    • 36749031067 scopus 로고    scopus 로고
    • Contact prediction using mutual information and neural nets
    • DOI 10.1002/prot.21791
    • Shackelford G, Karplus K (2007) Contact prediction using mutual information and neural nets. Proteins 69(Suppl 8):159-164 (Pubitemid 350210123)
    • (2007) Proteins: Structure, Function and Genetics , vol.69 , Issue.SUPPL. 8 , pp. 159-164
    • Shackelford, G.1    Karplus, K.2
  • 40
    • 47049101751 scopus 로고    scopus 로고
    • Using inferred residue contacts to distinguish between correct and incorrect protein models
    • DOI 10.1093/bioinformatics/btn248
    • Miller CS, Eisenberg D (2008) Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics 24:1575-1582 (Pubitemid 351966155)
    • (2008) Bioinformatics , vol.24 , Issue.14 , pp. 1575-1582
    • Miller, C.S.1    Eisenberg, D.2
  • 41
    • 42449129569 scopus 로고    scopus 로고
    • Information and discrimination in pairwise contact potentials
    • DOI 10.1002/prot.21733
    • Solis AD, Rackovsky S (2008) Information and discrimination in pairwise contact potentials. Proteins 71:1071-1087 (Pubitemid 351564035)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.3 , pp. 1071-1087
    • Solis, A.D.1    Rackovsky, S.2


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