메뉴 건너뛰기




Volumn 6, Issue 3, 2011, Pages

Novel feature for catalytic protein residues reflecting interactions with other residues

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROPTEROATE SYNTHASE; GLUTAREDOXIN; PROTEIN;

EID: 79953186069     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016932     Document Type: Article
Times cited : (13)

References (45)
  • 1
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • Capra JA, Singh M, (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23: 1875-1882.
    • (2007) Bioinformatics , vol.23 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 2
    • 6944227836 scopus 로고    scopus 로고
    • Automated prediction of protein function and detection of functional sites from structure
    • Pazos F, Sternberg MJE, (2004) Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci USA 101: 14754-14759.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14754-14759
    • Pazos, F.1    Sternberg, M.J.E.2
  • 4
    • 39749083945 scopus 로고    scopus 로고
    • A cavity with an appropriate size is the basis of the PPIase activity
    • Ikura T, Kinoshita K, Ito N, (2008) A cavity with an appropriate size is the basis of the PPIase activity. Protein Eng Des Sel 21: 83-89.
    • (2008) Protein Eng Des Sel , vol.21 , pp. 83-89
    • Ikura, T.1    Kinoshita, K.2    Ito, N.3
  • 5
    • 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 enzymeligand interfaces
    • BenShimon A, 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 enzymeligand interfaces. J Mol Biol 351: 309-326.
    • (2005) J Mol Biol , vol.351 , pp. 309-326
    • BenShimon, A.1    Eisenstein, M.2
  • 6
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge A, Bartlett GJ, Thornton JM, (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
  • 7
    • 33746950964 scopus 로고    scopus 로고
    • Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
    • Petrova NV, Wu CH, (2006) Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinformatics 7.
    • (2006) BMC Bioinformatics , vol.7
    • Petrova, N.V.1    Wu, C.H.2
  • 8
    • 48849085285 scopus 로고    scopus 로고
    • An improved prediction of catalytic residues in enzyme structures
    • Tang YR, Sheng ZY, Chen YZ, Zhang ZD, (2008) An improved prediction of catalytic residues in enzyme structures. Protein Eng Des Sel 21: 295-302.
    • (2008) Protein Eng Des Sel , vol.21 , pp. 295-302
    • Tang, Y.R.1    Sheng, Z.Y.2    Chen, Y.Z.3    Zhang, Z.D.4
  • 9
    • 38749104235 scopus 로고    scopus 로고
    • Identification of catalytic residues from protein structure using support vector machine with sequence and structural features
    • Pugalenthi G, Kumar KK, Suganthan PN, Gangal R, (2008) Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem Biophys Res Commun 367: 630-634.
    • (2008) Biochem Biophys Res Commun , vol.367 , pp. 630-634
    • Pugalenthi, G.1    Kumar, K.K.2    Suganthan, P.N.3    Gangal, R.4
  • 10
    • 40049091146 scopus 로고    scopus 로고
    • Prediction of protein functional residues from sequence by probability density estimation
    • Fischer JD, Mayer CE, Soding J, (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24: 613-620.
    • (2008) Bioinformatics , vol.24 , pp. 613-620
    • Fischer, J.D.1    Mayer, C.E.2    Soding, J.3
  • 11
    • 53749083563 scopus 로고    scopus 로고
    • Accurate sequencebased prediction of catalytic residues
    • Zhang T, Zhang H, Chen K, Shen S, Ruan J, et al. (2008) Accurate sequencebased prediction of catalytic residues. Bioinformatics 24: 2329-2338.
    • (2008) Bioinformatics , vol.24 , pp. 2329-2338
    • Zhang, T.1    Zhang, H.2    Chen, K.3    Shen, S.4    Ruan, J.5
  • 12
    • 33846554792 scopus 로고    scopus 로고
    • Evaluation of features for catalytic residue prediction in novel folds
    • Youn E, Peters B, Radivojac P, Mooney SD, (2007) Evaluation of features for catalytic residue prediction in novel folds. Protein Sci 16: 216-226.
    • (2007) Protein Sci , vol.16 , pp. 216-226
    • Youn, E.1    Peters, B.2    Radivojac, P.3    Mooney, S.D.4
  • 13
    • 35948961101 scopus 로고    scopus 로고
    • Predicting and annotating catalytic residues An information theoretic approach
    • Sterner B, Singh R, Berger B, (2007) Predicting and annotating catalytic residues An information theoretic approach. J Comput Biol 14: 1058-1073.
    • (2007) J Comput Biol , vol.14 , pp. 1058-1073
    • Sterner, B.1    Singh, R.2    Berger, B.3
  • 15
    • 4143145197 scopus 로고    scopus 로고
    • Finding functional sites in structural genomics proteins
    • Stark A, Shkumatov A, Russell RB, (2004) Finding functional sites in structural genomics proteins. Structure 12: 1405-1412.
    • (2004) Structure , vol.12 , pp. 1405-1412
    • Stark, A.1    Shkumatov, A.2    Russell, R.B.3
  • 16
    • 0037459071 scopus 로고    scopus 로고
    • Functional sites in protein families uncovered via an objective and automated graph theoretic approach
    • Wangikar PP, Tendulkar AV, Ramya S, Mail DN, Sarawagi S, (2003) Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J Mol Biol 326: 955-978.
    • (2003) J Mol Biol , vol.326 , pp. 955-978
    • Wangikar, P.P.1    Tendulkar, A.V.2    Ramya, S.3    Mail, D.N.4    Sarawagi, S.5
  • 17
    • 34547598665 scopus 로고    scopus 로고
    • PAR3D a server to predict protein active site residues
    • Goyal K, Mohanty D, Mande SC, (2007) PAR3D a server to predict protein active site residues. Nucleic Acids Res 35: W503-W505.
    • (2007) Nucleic Acids Res , vol.35
    • Goyal, K.1    Mohanty, D.2    Mande, S.C.3
  • 18
    • 14744305761 scopus 로고    scopus 로고
    • Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families
    • Torrance JW, Bartlett GJ, Porter CT, Thornton JM, (2005) Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 347: 565-581.
    • (2005) J Mol Biol , vol.347 , pp. 565-581
    • Torrance, J.W.1    Bartlett, G.J.2    Porter, C.T.3    Thornton, J.M.4
  • 19
    • 11344278220 scopus 로고    scopus 로고
    • Predicting protein functional sites with phylogenetic motifs
    • La D, Sutch B, Livesay DR, (2005) Predicting protein functional sites with phylogenetic motifs. Proteins 58: 309-320.
    • (2005) Proteins , vol.58 , pp. 309-320
    • La, D.1    Sutch, B.2    Livesay, D.R.3
  • 20
    • 33947393946 scopus 로고    scopus 로고
    • Locating the active sites of enzymes using mechanical properties
    • SacquinMora S, Laforet E, Lavery R, (2007) Locating the active sites of enzymes using mechanical properties. Proteins 67: 350-359.
    • (2007) Proteins , vol.67 , pp. 350-359
    • SacquinMora, S.1    Laforet, E.2    Lavery, R.3
  • 21
    • 59149090849 scopus 로고    scopus 로고
    • Partial Order Optimum Likelihood POOL Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
    • Tong WX, Wei Y, Murga LF, Ondrechen MJ, Williams RJ, (2009) Partial Order Optimum Likelihood POOL Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties. PLoS Comp Biol 5.
    • (2009) PLoS Comp Biol , vol.5
    • Tong, W.X.1    Wei, Y.2    Murga, L.F.3    Ondrechen, M.J.4    Williams, R.J.5
  • 22
    • 29144533902 scopus 로고    scopus 로고
    • Prediction of active sites for protein structures from computed chemical properties
    • Ko J, Murga LF, Wei Y, Ondrechen MJ, (2005) Prediction of active sites for protein structures from computed chemical properties. Bioinformatics 21: I258-I265.
    • (2005) Bioinformatics , vol.21
    • Ko, J.1    Murga, L.F.2    Wei, Y.3    Ondrechen, M.J.4
  • 23
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS A simple computational predictor of enzyme function from structure
    • Ondrechen MJ, Clifton JG, Ringe D, (2001) THEMATICS A simple computational predictor of enzyme function from structure. Proc Natl Acad Sci USA 98: 12473-12478.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 12473-12478
    • Ondrechen, M.J.1    Clifton, J.G.2    Ringe, D.3
  • 24
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene LH, Higman VA, (2003) Uncovering network systems within protein structures. J Mol Biol 334: 781-791.
    • (2003) J Mol Biol , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 25
    • 9944223645 scopus 로고    scopus 로고
    • Network properties of protein structures
    • Bagler G, Sinha S, (2005) Network properties of protein structures. Phys Stat Mech Appl 346: 27-33.
    • (2005) Phys Stat Mech Appl , vol.346 , pp. 27-33
    • Bagler, G.1    Sinha, S.2
  • 27
    • 41349118690 scopus 로고    scopus 로고
    • Smallworld view of the amino acids that play a key role in protein folding
    • Vendruscolo M, Dokholyan NV, Paci E, Karplus M, (2002) Smallworld view of the amino acids that play a key role in protein folding. Phys Rev E 65.
    • (2002) Phys Rev E , vol.65
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 28
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo M, Paci E, Dobson CM, Karplus M, (2001) Three key residues form a critical contact network in a protein folding transition state. Nature 409: 641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 29
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures Implications for protein stability
    • Brinda KV, Vishveshwara S, (2005) A network representation of protein structures Implications for protein stability. Biophys J 89: 4159-4170.
    • (2005) Biophys J , vol.89 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 30
    • 8544221118 scopus 로고    scopus 로고
    • Network analysis of protein structures identifies functional residues
    • Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, et al. (2004) Network analysis of protein structures identifies functional residues. J Mol Biol 344: 1135-1146.
    • (2004) J Mol Biol , vol.344 , pp. 1135-1146
    • Amitai, G.1    Shemesh, A.2    Sitbon, E.3    Shklar, M.4    Netanely, D.5
  • 31
    • 33748207211 scopus 로고    scopus 로고
    • Residue centrality, functionally important residues, and active site shape Analysis of enzyme and nonenzyme families
    • del Sol A, Fujihashi H, Amoros D, Nussinov R, (2006) Residue centrality, functionally important residues, and active site shape Analysis of enzyme and nonenzyme families. Protein Sci 15: 2120-2128.
    • (2006) Protein Sci , vol.15 , pp. 2120-2128
    • del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 34
    • 27144551715 scopus 로고    scopus 로고
    • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
    • Cheng G, Qian B, Samudrala R, Baker D, (2005) Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res 33: 5861-5867.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5861-5867
    • Cheng, G.1    Qian, B.2    Samudrala, R.3    Baker, D.4
  • 36
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon I, Weston J, Barnhill S, Vapnik V, (2002) Gene selection for cancer classification using support vector machines. Mach Learn 46: 389-422.
    • (2002) Mach Learn , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 37
    • 34249308113 scopus 로고    scopus 로고
    • How accurate and statistically robust are catalytic site predictions based on closeness centrality
    • Chea E, Livesay DR, (2007) How accurate and statistically robust are catalytic site predictions based on closeness centrality BMC Bioinformatics 8.
    • (2007) BMC Bioinformatics , vol.8
    • Chea, E.1    Livesay, D.R.2
  • 38
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas a resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, Thornton JM, (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
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 39
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSIBLAST a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSIBLAST a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.H.4    Zhang, Z.5
  • 40
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure patternrecognition of hydrogenbonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure patternrecognition of hydrogenbonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 41
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Gabor C, Tamas N, (2006) The igraph software package for complex network research. InterJournal Complex Systems pp. 1695.
    • (2006) InterJournal Complex Systems , pp. 1695
    • Gabor, C.1    Tamas, N.2
  • 42
    • 0038718854 scopus 로고    scopus 로고
    • The structure and function of complex networks
    • Newman MEJ, (2003) The structure and function of complex networks. SIAM Rev 45: 167-256.
    • (2003) SIAM Rev , vol.45 , pp. 167-256
    • Newman, M.E.J.1
  • 43
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of smallworld networks
    • Watts DJ, Strogatz SH, (1998) Collective dynamics of smallworld networks. Nature 393: 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 44
    • 4243148480 scopus 로고    scopus 로고
    • Authoritative sources in a hyperlinked environment
    • Kleinberg JM, (1999) Authoritative sources in a hyperlinked environment. J ACM 46: 604-632.
    • (1999) J ACM , vol.46 , pp. 604-632
    • Kleinberg, J.M.1
  • 45
    • 6344265551 scopus 로고    scopus 로고
    • Structural holes and good ideas
    • Burt RS, (2004) Structural holes and good ideas. Am J Sociology 110: 349-399.
    • (2004) Am J Sociology , vol.110 , pp. 349-399
    • Burt, R.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.