메뉴 건너뛰기




Volumn 24, Issue 20, 2008, Pages 2308-2316

Improving position-specific predictions of protein functional sites using phylogenetic motifs

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BINDING SITE; COMPUTER PREDICTION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME BINDING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; QUALITY CONTROL; QUANTITATIVE ANALYSIS; SCORING SYSTEM; SEQUENCE ALIGNMENT;

EID: 53749096681     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn454     Document Type: Article
Times cited : (16)

References (47)
  • 1
    • 0036384269 scopus 로고    scopus 로고
    • Simple physical models connect theory and experiment in protein folding kinetics
    • Alm,E. et al. (2002) Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol., 322, 463-476.
    • (2002) J. Mol. Biol , vol.322 , pp. 463-476
    • Alm, E.1
  • 2
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy,P. et al. (2001) Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311, 395-408.
    • (2001) J. Mol. Biol , vol.311 , pp. 395-408
    • Aloy, P.1
  • 3
    • 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, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 4
    • 8544221118 scopus 로고    scopus 로고
    • Network analysis of protein structures identifies functional residues
    • Amitai,G. 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
  • 5
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom,N. et al. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol., 294 1351-1362.
    • (1999) J. Mol. Biol , vol.294 , pp. 1351-1362
    • Blom, N.1
  • 6
    • 0037255072 scopus 로고    scopus 로고
    • The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    • Boeckmann,B. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
    • (2003) Nucleic Acids Res , vol.31 , pp. 365-370
    • Boeckmann, B.1
  • 7
    • 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
  • 8
    • 2642547217 scopus 로고    scopus 로고
    • Identify catalytic triads of serine hydrolases by support vector machines
    • Cai,Y.D. et al. (2004) Identify catalytic triads of serine hydrolases by support vector machines. J. Theor. Biol., 228, 551-557.
    • (2004) J. Theor. Biol , vol.228 , pp. 551-557
    • Cai, Y.D.1
  • 9
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • Capra,J.A. and 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
  • 10
    • 34249308113 scopus 로고    scopus 로고
    • How accurate and statistically robust are catalytic site predictions based on closeness centrality?
    • Chea,E. and Livesay,D.R. (2007) How accurate and statistically robust are catalytic site predictions based on closeness centrality? BMC Bioinformatics, 8, 153.
    • (2007) BMC Bioinformatics , vol.8 , pp. 153
    • Chea, E.1    Livesay, D.R.2
  • 11
    • 4544230537 scopus 로고    scopus 로고
    • Distinguishing structural and functional restraints in evolution in order to identify interaction sites
    • Chelliah,V. et al. (2004) Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J. Mol. Biol., 342, 1487-1504.
    • (2004) J. Mol. Biol , vol.342 , pp. 1487-1504
    • Chelliah, V.1
  • 12
    • 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. et al. (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
  • 13
    • 0037470597 scopus 로고    scopus 로고
    • Automatic methods for predicting functionally important residues
    • del Sol,A. et al. (2003) Automatic methods for predicting functionally important residues. J. Mol. Biol., 326, 1289-1302.
    • (2003) J. Mol. Biol , vol.326 , pp. 1289-1302
    • del Sol, A.1
  • 14
    • 34250195718 scopus 로고    scopus 로고
    • Relating destabilizing regions to known functional sites in proteins
    • Dessailly,B.H. et al. (2007) Relating destabilizing regions to known functional sites in proteins. BMC Bioinformatics, 8, 141.
    • (2007) BMC Bioinformatics , vol.8 , pp. 141
    • Dessailly, B.H.1
  • 15
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock,A.H. (2001) Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312, 885-896.
    • (2001) J. Mol. Biol , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 16
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge,A. et al. (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
  • 17
    • 0034459679 scopus 로고    scopus 로고
    • Evolutionary trace analysis of TGF-β and related growth factors: Implications for site-directed mutagenesis
    • Innis,C.A. et al. (2000) Evolutionary trace analysis of TGF-β and related growth factors: Implications for site-directed mutagenesis. Prot. Eng., 13, 839-847.
    • (2000) Prot. Eng , vol.13 , pp. 839-847
    • Innis, C.A.1
  • 18
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman,B. and Baker,D. (2000) Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA, 97, 10383-10388.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 19
    • 23144444422 scopus 로고    scopus 로고
    • La,D. and Livesay,D.R. (2005) MINER: Software for phylogenetic motif identification. Nucleic Acids Res., 33, W267-W270.
    • La,D. and Livesay,D.R. (2005) MINER: Software for phylogenetic motif identification. Nucleic Acids Res., 33, W267-W270.
  • 20
    • 25444468321 scopus 로고    scopus 로고
    • La,D. and Livesay,D.R. (2005) Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics, 6, 116.
    • La,D. and Livesay,D.R. (2005) Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics, 6, 116.
  • 21
    • 11344278220 scopus 로고    scopus 로고
    • La,D. et al. (2005) Predicting protein functional sites with phylogenetic motifs. Proteins, 58, 309-320.
    • La,D. et al. (2005) Predicting protein functional sites with phylogenetic motifs. Proteins, 58, 309-320.
  • 22
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge,O. et al. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257 342-358.
    • (1996) J. Mol. Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1
  • 23
    • 17744397525 scopus 로고    scopus 로고
    • Livesay,D.R. and La,D. (2005) The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins. Protein Sci., 14, 1158-1170.
    • Livesay,D.R. and La,D. (2005) The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins. Protein Sci., 14, 1158-1170.
  • 24
    • 38049173153 scopus 로고    scopus 로고
    • Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: A case study analyzing the neurotransmitter/Na+ symporter family
    • Livesay,D.R. et al. (2007) Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. BMC Bioinformatics, 8, 397.
    • (2007) BMC Bioinformatics , vol.8 , pp. 397
    • Livesay, D.R.1
  • 25
    • 0036300444 scopus 로고    scopus 로고
    • Structural clusters of evolutionary trace residues are statistically significant and common in proteins
    • Madabushi,S. et al. (2002) Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J. Mol. Biol., 316, 139-154.
    • (2002) J. Mol. Biol , vol.316 , pp. 139-154
    • Madabushi, S.1
  • 26
    • 1542379652 scopus 로고    scopus 로고
    • Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions
    • Madabushi,S. et al. (2004) Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J. Biol. Chem., 279, 8126-8132.
    • (2004) J. Biol. Chem , vol.279 , pp. 8126-8132
    • Madabushi, S.1
  • 27
    • 40749144489 scopus 로고    scopus 로고
    • The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
    • Manning,J.R. et al. (2008) The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics, 9, 51.
    • (2008) BMC Bioinformatics , vol.9 , pp. 51
    • Manning, J.R.1
  • 28
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior
    • Mayrose,I. et al. (2004) Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Mol. Biol. Evol., 21, 1781-1791.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1781-1791
    • Mayrose, I.1
  • 29
    • 0000596361 scopus 로고
    • Note on the sampling error of the difference between correlated proportions or percentages
    • McNemar,Q. (1947) Note on the sampling error of the difference between correlated proportions or percentages. Psychometrika, 12, 153-157.
    • (1947) Psychometrika , vol.12 , pp. 153-157
    • McNemar, Q.1
  • 30
    • 1242339659 scopus 로고    scopus 로고
    • A family of evolution-entropy hybrid methods for ranking protein residues by importance
    • Mihalek,I. et al. (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J. Mol. Biol., 336, 1265-1282.
    • (2004) J. Mol. Biol , vol.336 , pp. 1265-1282
    • Mihalek, I.1
  • 31
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald,I.K. and Thorton,J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
    • (1994) J. Mol. Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thorton, J.M.2
  • 32
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • Ondrechen,M.J. et al. (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
  • 34
    • 33846220351 scopus 로고    scopus 로고
    • Computational prediction of functionally important regions in proteins
    • Pazos,F. and Bang,J. (2006) Computational prediction of functionally important regions in proteins. Curr. Bioinformatics, 1, 15-23.
    • (2006) Curr. Bioinformatics , vol.1 , pp. 15-23
    • Pazos, F.1    Bang, J.2
  • 35
    • 33745599119 scopus 로고    scopus 로고
    • Phylogeny-independent detection of functional residues
    • Pazos,F. et al. (2006) Phylogeny-independent detection of functional residues. Bioinformatics, 22, 1440-1448.
    • (2006) Bioinformatics , vol.22 , pp. 1440-1448
    • Pazos, F.1
  • 36
    • 0141705410 scopus 로고    scopus 로고
    • Using protein design for homology detection and active site searches
    • Pei,J. et al. (2003) Using protein design for homology detection and active site searches. Proc. Natl Acad. Sci. USA, 100, 11361-11366.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 11361-11366
    • Pei, J.1
  • 37
    • 33746950964 scopus 로고    scopus 로고
    • Prediction of catalytic residues using Support vector machine with selected protein sequence and structural properties
    • Petrova,N.V. and Wu,C.H. (2006) Prediction of catalytic residues using Support vector machine with selected protein sequence and structural properties. BMC Bioinformatics, 7, 312.
    • (2006) BMC Bioinformatics , vol.7 , pp. 312
    • Petrova, N.V.1    Wu, C.H.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,C.T. et al. (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
  • 39
    • 0033613817 scopus 로고    scopus 로고
    • Evolutionary trace analysis of the Kunitz/BPTI family of proteins: Functional divergence may have been based on conformational adjustment
    • Pritchard,L. and Dufton,M.J. (1999) Evolutionary trace analysis of the Kunitz/BPTI family of proteins: Functional divergence may have been based on conformational adjustment. J. Mol. Biol., 285, 1589-1607.
    • (1999) J. Mol. Biol , vol.285 , pp. 1589-1607
    • Pritchard, L.1    Dufton, M.J.2
  • 40
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko,T. et al. (2002) Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18, S71-S77.
    • (2002) Bioinformatics , vol.18
    • Pupko, T.1
  • 42
    • 0035126520 scopus 로고    scopus 로고
    • Prediction and confirmation of a site critical for effector regulation of RGS domain activity
    • Sowa,M.E. et al. (2001) Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nat. Struct. Biol., 8, 234-237.
    • (2001) Nat. Struct. Biol , vol.8 , pp. 234-237
    • Sowa, M.E.1
  • 43
    • 25444527443 scopus 로고    scopus 로고
    • Improved prediction of critical residues for protein function based on network and phylogenetic analyses
    • Thibert,B. et al. (2005) Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics, 6, 213.
    • (2005) BMC Bioinformatics , vol.6 , pp. 213
    • Thibert, B.1
  • 44
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar,W.S. (2002) Scoring residue conservation. Proteins, 48 227-241.
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.1
  • 45
    • 46049119818 scopus 로고    scopus 로고
    • StAR: A simple tool for the statistical comparison of ROC curves
    • Vergara,I.A. et al. (2008) StAR: A simple tool for the statistical comparison of ROC curves. BMC Bioinformatics, 9, 265.
    • (2008) BMC Bioinformatics , vol.9 , pp. 265
    • Vergara, I.A.1
  • 46
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • Watson,J.D. et al. (2005) Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol., 15, 275-284.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 275-284
    • Watson, J.D.1
  • 47
    • 0037423759 scopus 로고    scopus 로고
    • An accurate, sensitive, and scalable method to identify functional sites in protein structures
    • Yao,H. et al. (2003) An accurate, sensitive, and scalable method to identify functional sites in protein structures. J. Mol. Biol., 326, 255-261.
    • (2003) J. Mol. Biol , vol.326 , pp. 255-261
    • Yao, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.