메뉴 건너뛰기




Volumn 79, Issue 3, 2011, Pages 888-897

Prediction of protein binding regions

Author keywords

Genetic engineering; Molecular simulation; Protein aggregation; Protein protein interactions; Spatial aggregation propensity

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; FC RECEPTOR; IMMUNOGLOBULIN G1 ANTIBODY; PROTEIN A; PROTEIN G; TRANSFORMING GROWTH FACTOR ALPHA;

EID: 79551480295     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22926     Document Type: Article
Times cited : (16)

References (53)
  • 1
    • 33644836724 scopus 로고    scopus 로고
    • Epidermal growth factor receptor inhibition for the treatment of glioblastoma multiforme and other malignant brain tumours
    • Halatsch ME, Schmidt U, Behnke-Mursch J, Unterberg A, Wirtz CR. Epidermal growth factor receptor inhibition for the treatment of glioblastoma multiforme and other malignant brain tumours. Cancer Treat Rev 2006; 32: 74-89.
    • (2006) Cancer Treat Rev , vol.32 , pp. 74-89
    • Halatsch, M.E.1    Schmidt, U.2    Behnke-Mursch, J.3    Unterberg, A.4    Wirtz, C.R.5
  • 2
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: expectations and outcomes
    • Chandonia JM, Brenner SE. The impact of structural genomics: expectations and outcomes. Science 2006; 311: 347-351.
    • (2006) Science , vol.311 , pp. 347-351
    • Chandonia, J.M.1    Brenner, S.E.2
  • 3
    • 0033762915 scopus 로고    scopus 로고
    • Structural genomics programs at the US National Institute of General Medical Sciences
    • Norvell JC, Machalek AZ. Structural genomics programs at the US National Institute of General Medical Sciences. Nat Struct Biol 2000; 7: 931.
    • (2000) Nat Struct Biol , vol.7 , pp. 931
    • Norvell, J.C.1    Machalek, A.Z.2
  • 4
    • 0033757870 scopus 로고    scopus 로고
    • Structural genomics in North America
    • Terwilliger TC. Structural genomics in North America. Nat Struct Biol 2000; 7: 935-939.
    • (2000) Nat Struct Biol , vol.7 , pp. 935-939
    • Terwilliger, T.C.1
  • 6
    • 1042264059 scopus 로고    scopus 로고
    • Searching for functional sites in protein structures
    • Jones S, Thornton JM. Searching for functional sites in protein structures. Curr Opin Chem Biol 2004; 8: 3-7.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 3-7
    • Jones, S.1    Thornton, J.M.2
  • 7
    • 49049105131 scopus 로고    scopus 로고
    • Using protein binding site prediction to improve protein docking
    • Huang B, Schroeder M. Using protein binding site prediction to improve protein docking. Gene 2008; 422: 14-21.
    • (2008) Gene , vol.422 , pp. 14-21
    • Huang, B.1    Schroeder, M.2
  • 8
    • 33646044395 scopus 로고    scopus 로고
    • WHISCY: what information does surface conservation yield? Application to data-driven docking
    • Vries SD, van Dirj A, Bonvin A. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins 2006; 63: 479-489.
    • (2006) Proteins , vol.63 , pp. 479-489
    • Vries, S.D.1    van Dirj, A.2    Bonvin, A.3
  • 9
    • 1842595135 scopus 로고    scopus 로고
    • A novel method for scoring of docked protein complexes using predicted protein-protein binding sites
    • Gottschalk K, Neuvirth H, Schreiber G. A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng 2004; 17: 183-189.
    • (2004) Protein Eng , vol.17 , pp. 183-189
    • Gottschalk, K.1    Neuvirth, H.2    Schreiber, G.3
  • 10
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: an overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002; 47: 409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 11
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. Dominant forces in protein folding. Biochemistry 1990; 31: 7134-7155.
    • (1990) Biochemistry , vol.31 , pp. 7134-7155
    • Dill, K.A.1
  • 12
    • 27344440132 scopus 로고    scopus 로고
    • Conservation and relative importance of residues across protein-protein interfaces
    • Guharoy M, Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc Natl Acad Sci USA 2005; 43: 15447-15452.
    • (2005) Proc Natl Acad Sci USA , vol.43 , pp. 15447-15452
    • Guharoy, M.1    Chakrabarti, P.2
  • 13
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996; 93: 13-20.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 14
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 1994; 3: 717-729.
    • (1994) Protein Sci , vol.3 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 15
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect
    • Tsai C, Lin SL, Wolfson HJ, Nussinov R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci 1997; 6: 53-64.
    • (1997) Protein Sci , vol.6 , pp. 53-64
    • Tsai, C.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 16
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Conte LL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999; 285: 2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 17
    • 0034681465 scopus 로고    scopus 로고
    • Convergent solutions to binding at a protein-protein interface
    • DeLano WL, Ultsch MH, de Vos AM, Wells JA. Convergent solutions to binding at a protein-protein interface. Science 2000; 287: 1279-1283.
    • (2000) Science , vol.287 , pp. 1279-1283
    • DeLano, W.L.1    Ultsch, M.H.2    de Vos, A.M.3    Wells, J.A.4
  • 18
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren IM, Thornton JM. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 2003; 325: 991-1018.
    • (2003) J Mol Biol , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 19
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001; 43: 89-102.
    • (2001) Proteins , vol.43 , pp. 89-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 20
    • 0032522670 scopus 로고    scopus 로고
    • Morphology of protein-protein interfaces
    • Larsen TA, Olson AJ, Goodsell DS. Morphology of protein-protein interfaces. Structure 1998; 6: 421-427.
    • (1998) Structure , vol.6 , pp. 421-427
    • Larsen, T.A.1    Olson, A.J.2    Goodsell, D.S.3
  • 21
    • 59149087824 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites in sequences and 3D structures by random forests
    • Šikić M, Tomić S, Vlahoviček K. Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 2009; 5: e1000278.
    • (2009) PLoS Comput Biol , vol.5
    • Šikić, M.1    Tomić, S.2    Vlahoviček, K.3
  • 22
    • 33846662784 scopus 로고    scopus 로고
    • ISIS: interaction sites identified from sequence
    • Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics 2007; 23: e13-e16.
    • (2007) Bioinformatics , vol.23
    • Ofran, Y.1    Rost, B.2
  • 23
    • 19544369864 scopus 로고    scopus 로고
    • An evolution based classifier for prediction of protein interfaces without using protein structures
    • Res I, Mihalek I, Lichtarge O. An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 2005; 21: 2496-2501.
    • (2005) Bioinformatics , vol.21 , pp. 2496-2501
    • Res, I.1    Mihalek, I.2    Lichtarge, O.3
  • 24
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucl Acids Res 2006; 34: 3698-3707.
    • (2006) Nucl Acids Res , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4
  • 25
    • 33846200437 scopus 로고    scopus 로고
    • Prediction-based finger-prints of protein-protein interactions
    • Porollo A, Meller J. Prediction-based finger-prints of protein-protein interactions. Proteins 2007; 66: 630-645.
    • (2007) Proteins , vol.66 , pp. 630-645
    • Porollo, A.1    Meller, J.2
  • 26
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005; 21: 1487-1494.
    • (2005) Bioinformatics , vol.21 , pp. 1487-1494
    • Bradford, J.R.1    Westhead, D.R.2
  • 27
    • 24344484686 scopus 로고    scopus 로고
    • Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
    • Chen H, Zhou HX. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005; 61: 21-35.
    • (2005) Proteins , vol.61 , pp. 21-35
    • Chen, H.1    Zhou, H.X.2
  • 28
    • 20844454090 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
    • Aytuna AS, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 2005; 21: 2850-2855.
    • (2005) Bioinformatics , vol.21 , pp. 2850-2855
    • Aytuna, A.S.1    Gursoy, A.2    Keskin, O.3
  • 29
    • 1842526090 scopus 로고    scopus 로고
    • Promate: a structure based prediction program to identify the location of protein-protein binding sites
    • H. Neuvirth, R. Raz, Schreiber, G. Promate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004; 338: 181-199.
    • (2004) J Mol Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 30
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997; 272: 133-143.
    • (1997) J Mol Biol , vol.272 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 31
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 2002; 12: 21-27.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 32
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003; 19: 163-164.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 33
    • 38549092067 scopus 로고    scopus 로고
    • HotSprint: database of computational HotSpots at protein interfaces
    • Guney E, Tuncbag N, Keskin O, Gursoy A. HotSprint: database of computational HotSpots at protein interfaces. Nucl Acids Res 2007; 36: D662-D666.
    • (2007) Nucl Acids Res , vol.36
    • Guney, E.1    Tuncbag, N.2    Keskin, O.3    Gursoy, A.4
  • 34
    • 0037022603 scopus 로고    scopus 로고
    • Inference of functional regions in proteins by quantification of evolutionary constraints
    • Simon AL, Stone EA, Sidow A. Inference of functional regions in proteins by quantification of evolutionary constraints. Proc Natl Acad Sci USA 2002; 99: 2912-2917.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 2912-2917
    • Simon, A.L.1    Stone, E.A.2    Sidow, A.3
  • 37
    • 77952471578 scopus 로고    scopus 로고
    • Predictive tools for stabilization of therapeutic proteins
    • Voynov V, Chennamsetty N, Kayser V, Helk B, Trout BL. Predictive tools for stabilization of therapeutic proteins. MAbs 2009; 1: 580-582.
    • (2009) MAbs , vol.1 , pp. 580-582
    • Voynov, V.1    Chennamsetty, N.2    Kayser, V.3    Helk, B.4    Trout, B.L.5
  • 44
    • 0036771632 scopus 로고    scopus 로고
    • Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations
    • Kuttel M, Brady JW, Naidoo KJ. Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem 2002; 23: 1236-1243.
    • (2002) J Comput Chem , vol.23 , pp. 1236-1243
    • Kuttel, M.1    Brady, J.W.2    Naidoo, K.J.3
  • 45
    • 0026069154 scopus 로고
    • Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications
    • Black SD, Mould DR. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. Anal Biochem 1991; 193: 72-82.
    • (1991) Anal Biochem , vol.193 , pp. 72-82
    • Black, S.D.1    Mould, D.R.2
  • 47
    • 0018173811 scopus 로고
    • Crystallization, crystal structure analysis and atomic model of the complex formed by a human Fc fragment and fragment B of protein A from Staphylococcus aureus
    • Deisenhofer J, Jones TA, Huber R, Sjodahl J, Sjoquist J. Crystallization, crystal structure analysis and atomic model of the complex formed by a human Fc fragment and fragment B of protein A from Staphylococcus aureus. Hoppe-Seyler's Z Physiol Chem 1978; 359: 975-985.
    • (1978) Hoppe-Seyler's Z Physiol Chem , vol.359 , pp. 975-985
    • Deisenhofer, J.1    Jones, T.A.2    Huber, R.3    Sjodahl, J.4    Sjoquist, J.5
  • 48
    • 0019522383 scopus 로고
    • Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution
    • Deisenhofer J. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. Biochemistry 1981; 20: 2361-2370.
    • (1981) Biochemistry , vol.20 , pp. 2361-2370
    • Deisenhofer, J.1
  • 49
    • 0029644247 scopus 로고
    • Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG
    • Sauer-Eriksson AE, Kleywegt GJ, Uhlen M, Jones TA. Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. Structure 1995; 3: 265-278.
    • (1995) Structure , vol.3 , pp. 265-278
    • Sauer-Eriksson, A.E.1    Kleywegt, G.J.2    Uhlen, M.3    Jones, T.A.4
  • 50
    • 67649852558 scopus 로고    scopus 로고
    • Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins
    • Pechmann S, Levy ED, Tartaglia GG, Vendruscolo M. Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins. Proc Natl Acad Sci USA 2009; 106: 10159-10164.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10159-10164
    • Pechmann, S.1    Levy, E.D.2    Tartaglia, G.G.3    Vendruscolo, M.4
  • 51
    • 77952528356 scopus 로고    scopus 로고
    • Potential aggregation prone regions in biotherapeutics
    • Wang X, Das TK, Singh SK, Kumar S. Potential aggregation prone regions in biotherapeutics. MAbs 2009; 1: 1-14.
    • (2009) MAbs , vol.1 , pp. 1-14
    • Wang, X.1    Das, T.K.2    Singh, S.K.3    Kumar, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.