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Volumn 7, Issue 8, 2012, Pages

FunSAV: Predicting the functional effect of single amino acid variants using a two-stage random forest model

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CLASSIFIER; DISEASE ASSOCIATION; INTERMETHOD COMPARISON; PREDICTION; PROTEIN STRUCTURE; RANDOM FOREST; SINGLE AMINO ACID VARIANT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84865298225     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043847     Document Type: Article
Times cited : (50)

References (73)
  • 1
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • Durbin RM, Altshuler D, Abecasis GR, Bentley DR, (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
    • Durbin, R.M.1    Altshuler, D.2    Abecasis, G.R.3    Bentley, D.R.4
  • 2
    • 79951521614 scopus 로고    scopus 로고
    • Using bioinformatics to predict the functional impact of SNVs
    • Cline MS, Karchin R, (2011) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics 27: 441-448.
    • (2011) Bioinformatics , vol.27 , pp. 441-448
    • Cline, M.S.1    Karchin, R.2
  • 4
    • 69749124820 scopus 로고    scopus 로고
    • The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group
    • Ahn SM, Kim TH, Lee S, Kim D, Ghang H, et al. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 19: 1622-1629.
    • (2009) Genome Res , vol.19 , pp. 1622-1629
    • Ahn, S.M.1    Kim, T.H.2    Lee, S.3    Kim, D.4    Ghang, H.5
  • 5
    • 55549097849 scopus 로고    scopus 로고
    • The diploid genome sequence of an Asian individual
    • Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
    • (2008) Nature , vol.456 , pp. 60-65
    • Wang, J.1    Wang, W.2    Li, R.3    Li, Y.4    Tian, G.5
  • 6
    • 2342596530 scopus 로고    scopus 로고
    • The Swiss-Prot variant page and the ModSNP database: A resource for sequence and structure information on human protein variants
    • Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, et al. (2004) The Swiss-Prot variant page and the ModSNP database: A resource for sequence and structure information on human protein variants. Human Mutation 23: 464-470.
    • (2004) Human Mutation , vol.23 , pp. 464-470
    • Yip, Y.L.1    Scheib, H.2    Diemand, A.V.3    Gattiker, A.4    Famiglietti, L.M.5
  • 7
    • 0037373275 scopus 로고    scopus 로고
    • Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease
    • Botstein D, Risch N, (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33Suppl: 228-237.
    • (2003) Nat Genet , vol.33
    • Botstein, D.1    Risch, N.2
  • 9
    • 80054867468 scopus 로고    scopus 로고
    • Predicting functional impact of single amino acid polymorphisms by integrating sequence and structural features
    • Zhuhai, China: IEEE eXpress Conference Publishing
    • Wang M, Shen H-B, Akutsu T, Song J (2011) Predicting functional impact of single amino acid polymorphisms by integrating sequence and structural features. The 5th IEEE International Conference on Systems Biology (ISB 2011). Zhuhai, China: IEEE eXpress Conference Publishing. 18-26.
    • (2011) The 5th IEEE International Conference on Systems Biology (ISB 2011) , pp. 18-26
    • Wang, M.1    Shen, H.-B.2    Akutsu, T.3    Song, J.4
  • 10
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • Ng PC, Henikoff S, (2001) Predicting deleterious amino acid substitutions. Genome Res 11: 863-874.
    • (2001) Genome Res , vol.11 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 11
    • 0033387172 scopus 로고    scopus 로고
    • Prediction of nonsynonymous xsingle nucleotide polymorphisms in human disease-associated genes
    • Bork P, Sunyaev S, Hanke J, Aydin A, Wirkner U, et al. (1999) Prediction of nonsynonymous xsingle nucleotide polymorphisms in human disease-associated genes. J Mol Med 77: 754-760.
    • (1999) J Mol Med , vol.77 , pp. 754-760
    • Bork, P.1    Sunyaev, S.2    Hanke, J.3    Aydin, A.4    Wirkner, U.5
  • 12
    • 0032991552 scopus 로고    scopus 로고
    • Characterization of single-nucleotide polymorphisms in coding regions of human genes Nat Genet
    • Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes Nat Genet. 22: 231-238.
    • (1999) , vol.22 , pp. 231-238
    • Cargill, M.1    Altshuler, D.2    Ireland, J.3    Sklar, P.4    Ardlie, K.5
  • 13
    • 0035937259 scopus 로고    scopus 로고
    • Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation
    • Chasman D, Adams RM, (2001) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J Mol Biol 307: 683-706.
    • (2001) J Mol Biol , vol.307 , pp. 683-706
    • Chasman, D.1    Adams, R.M.2
  • 14
    • 0035065485 scopus 로고    scopus 로고
    • SNPs, protein structure, and disease
    • Wang Z, Moult J, (2001) SNPs, protein structure, and disease. Human Mutation 17: 263-270.
    • (2001) Human Mutation , vol.17 , pp. 263-270
    • Wang, Z.1    Moult, J.2
  • 15
    • 53749105617 scopus 로고    scopus 로고
    • SNAP predicts effect of mutations on protein function
    • Bromberg Y, Yachdav G, Rost B, (2008) SNAP predicts effect of mutations on protein function. Bioinformatics 24: 2397-2398.
    • (2008) Bioinformatics , vol.24 , pp. 2397-2398
    • Bromberg, Y.1    Yachdav, G.2    Rost, B.3
  • 16
    • 77954290402 scopus 로고    scopus 로고
    • MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data
    • Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, et al. (2010) MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res 38: 7869-7869.
    • (2010) Nucleic Acids Res , vol.38 , pp. 7869
    • Wainreb, G.1    Ashkenazy, H.2    Bromberg, Y.3    Starovolsky-Shitrit, A.4    Haliloglu, T.5
  • 17
    • 67749129254 scopus 로고    scopus 로고
    • Prediction of function changes associated with single-point protein mutations using support vector machines (SVMs)
    • Gao S, Zhang N, Duan GY, Yang Z, Ruan JS, et al. (2009) Prediction of function changes associated with single-point protein mutations using support vector machines (SVMs). Hum Mutat 30: 1161-1166.
    • (2009) Hum Mutat , vol.30 , pp. 1161-1166
    • Gao, S.1    Zhang, N.2    Duan, G.Y.3    Yang, Z.4    Ruan, J.S.5
  • 18
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: predicting amino acid changes that affect protein function
    • Ng PC, Henikoff S, (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 19
    • 0141742293 scopus 로고    scopus 로고
    • PANTHER: a library of protein families and subfamilies indexed by function
    • Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, et al. (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13: 2129-2141.
    • (2003) Genome Res , vol.13 , pp. 2129-2141
    • Thomas, P.D.1    Campbell, M.J.2    Kejariwal, A.3    Mi, H.4    Karlak, B.5
  • 20
    • 33751013750 scopus 로고    scopus 로고
    • Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
    • Capriotti E, Calabrese R, Casadio R, (2006) Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 22: 2729-2734.
    • (2006) Bioinformatics , vol.22 , pp. 2729-2734
    • Capriotti, E.1    Calabrese, R.2    Casadio, R.3
  • 21
    • 77949465285 scopus 로고    scopus 로고
    • Structural and functional restraints on the occurrence of single amino acid variations in human proteins
    • Gong S, Blundell TL, (2010) Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PloS One 5: e9186.
    • (2010) PloS One , vol.5
    • Gong, S.1    Blundell, T.L.2
  • 23
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA, (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33: D514-D517.
    • (2005) Nucleic Acids Res , vol.33
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 25
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • The International HapMap Consortium
    • The International HapMap Consortium, (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
    • (2007) Nature , vol.449 , pp. 851-861
  • 26
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 28
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, 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    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 29
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT, (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 30
  • 31
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life
    • Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT, (2004) Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life. J Mol Biol 337: 635-645.
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 32
    • 0033028454 scopus 로고    scopus 로고
    • PSIC: profile extraction from sequence alignments with position-specific counts of independent observations
    • Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, et al. (1999) PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng 12: 387-394.
    • (1999) Protein Eng , vol.12 , pp. 387-394
    • Sunyaev, S.R.1    Eisenhaber, F.2    Rodchenkov, I.V.3    Eisenhaber, B.4    Tumanyan, V.G.5
  • 33
    • 5044235541 scopus 로고    scopus 로고
    • Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    • Fernandez-Escamilla A-M, Rousseau F, Schymkowitz J, Serrano L, (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotech 22: 1302-1306.
    • (2004) Nat Biotech , vol.22 , pp. 1302-1306
    • Fernandez-Escamilla, A.-M.1    Rousseau, F.2    Schymkowitz, J.3    Serrano, L.4
  • 34
    • 34547840189 scopus 로고    scopus 로고
    • Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP)
    • Ye ZQ, Zhao S-Q, Gao G, Liu X-Q, Langlois RE, et al. (2007) Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP). Bioinformatics 23: 1444-1450.
    • (2007) Bioinformatics , vol.23 , pp. 1444-1450
    • Ye, Z.Q.1    Zhao, S.-Q.2    Gao, G.3    Liu, X.-Q.4    Langlois, R.E.5
  • 35
    • 46249133956 scopus 로고    scopus 로고
    • HSEpred: predict half-sphere exposure from protein sequences
    • Song J, Tan H, Takemoto K, Akutsu T, (2008) HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics 24: 1489-1497.
    • (2008) Bioinformatics , vol.24 , pp. 1489-1497
    • Song, J.1    Tan, H.2    Takemoto, K.3    Akutsu, T.4
  • 36
    • 77951972791 scopus 로고    scopus 로고
    • Cascleave: towards more accurate prediction of caspase substrate cleavage sites
    • Song J, Tan H, Shen H, Mahmood K, Boyd SE, et al. (2010) Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics 26: 752-760.
    • (2010) Bioinformatics , vol.26 , pp. 752-760
    • Song, J.1    Tan, H.2    Shen, H.3    Mahmood, K.4    Boyd, S.E.5
  • 37
    • 36549021546 scopus 로고    scopus 로고
    • Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
    • Song J, Yuan Z, Tan H, Huber T, Burrage K, (2007) Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinformatics 23: 3147-3154.
    • (2007) Bioinformatics , vol.23 , pp. 3147-3154
    • Song, J.1    Yuan, Z.2    Tan, H.3    Huber, T.4    Burrage, K.5
  • 38
    • 26944462332 scopus 로고    scopus 로고
    • A novel approach to extracting features from motif content and protein composition for protein sequence classification
    • Zhao XM, Cheung YM, Huang DS, (2005) A novel approach to extracting features from motif content and protein composition for protein sequence classification. Neural Netw 18: 1019-1028.
    • (2005) Neural Netw , vol.18 , pp. 1019-1028
    • Zhao, X.M.1    Cheung, Y.M.2    Huang, D.S.3
  • 39
    • 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
  • 40
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald IK, Thornton JM, (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    Thornton, J.M.2
  • 41
    • 0035504763 scopus 로고    scopus 로고
    • Understanding human disease mutations through the use of interspecific genetic variation
    • Miller MP, Kumar S, (2001) Understanding human disease mutations through the use of interspecific genetic variation. Hum Mol Genet 10: 2319-2328.
    • (2001) Hum Mol Genet , vol.10 , pp. 2319-2328
    • Miller, M.P.1    Kumar, S.2
  • 42
    • 78049444976 scopus 로고    scopus 로고
    • Correlated mutations: a hallmark of phenotypic amino acid substitutions
    • Kowarsch A, Fuchs A, Frishman D, Pagel P, (2010) Correlated mutations: a hallmark of phenotypic amino acid substitutions. PLoS Comput Biol 6: e1000923.
    • (2010) PLoS Comput Biol , vol.6
    • Kowarsch, A.1    Fuchs, A.2    Frishman, D.3    Pagel, P.4
  • 43
    • 0027297096 scopus 로고
    • Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis
    • Korber BT, Farber RM, Wolpert DH, Lapedes AS, (1993) Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc Natl Acad Sci USA 90: 7176-7180.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 7176-7180
    • Korber, B.T.1    Farber, R.M.2    Wolpert, D.H.3    Lapedes, A.S.4
  • 44
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • Martin LC, Gloor GB, Dunn SD, Wahl LM, (2005) Using information theory to search for co-evolving residues in proteins. Bioinformatics 21: 4116-4124.
    • (2005) Bioinformatics , vol.21 , pp. 4116-4124
    • Martin, L.C.1    Gloor, G.B.2    Dunn, S.D.3    Wahl, L.M.4
  • 45
    • 38849115223 scopus 로고    scopus 로고
    • Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    • Dunn SD, Wahl LM, Gloor GB, (2008) Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction. Bioinformatics 24: 333-340.
    • (2008) Bioinformatics , vol.24 , pp. 333-340
    • Dunn, S.D.1    Wahl, L.M.2    Gloor, G.B.3
  • 46
    • 0034721944 scopus 로고    scopus 로고
    • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
    • Larson SM, Di Nardo AA, Davidson AR, (2000) Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J Mol Biol 303: 433-446.
    • (2000) J Mol Biol , vol.303 , pp. 433-446
    • Larson, S.M.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 47
    • 78651230959 scopus 로고    scopus 로고
    • Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
    • Li YZ, Wen ZN, Xiao JM, Yin H, Yu LZ, et al. (2011) Predicting disease-associated substitution of a single amino acid by analyzing residue interactions. BMC Bioinformatics 12: 14.
    • (2011) BMC Bioinformatics , vol.12 , pp. 14
    • Li, Y.Z.1    Wen, Z.N.2    Xiao, J.M.3    Yin, H.4    Yu, L.Z.5
  • 48
    • 33745862379 scopus 로고    scopus 로고
    • Predicting deleterious nsSNPs: an analysis of sequence and structural attributes
    • Dobson R, Munroe P, Caulfield M, Saqi M, (2006) Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. BMC Bioinformatics 7: 217.
    • (2006) BMC Bioinformatics , vol.7 , pp. 217
    • Dobson, R.1    Munroe, P.2    Caulfield, M.3    Saqi, M.4
  • 49
    • 0036387236 scopus 로고    scopus 로고
    • Evaluation of Structural and Evolutionary Contributions to Deleterious Mutation Prediction
    • Saunders CT, Baker D, (2002) Evaluation of Structural and Evolutionary Contributions to Deleterious Mutation Prediction. J Mol Biol 322: 891-901.
    • (2002) J Mol Biol , vol.322 , pp. 891-901
    • Saunders, C.T.1    Baker, D.2
  • 51
    • 14644400399 scopus 로고    scopus 로고
    • An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
    • Hamelryck T, (2005) An amino acid has two sides: A new 2D measure provides a different view of solvent exposure. Proteins 59: 38-48.
    • (2005) Proteins , vol.59 , pp. 38-48
    • Hamelryck, T.1
  • 53
    • 23144437332 scopus 로고    scopus 로고
    • nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms
    • Bao L, Zhou M, Cui Y, (2005) nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Res 33: W480-W482.
    • (2005) Nucleic Acids Res , vol.33
    • Bao, L.1    Zhou, M.2    Cui, Y.3
  • 54
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW, (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta-Protein Structure 405: 442-451.
    • (1975) Biochim Biophys Acta-Protein Structure , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 55
    • 0345040873 scopus 로고    scopus 로고
    • Classification and Regression by randomForest
    • Liaw A, Wiener M, (2002) Classification and Regression by randomForest. R news 2: 18-22.
    • (2002) R News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 56
    • 5644254728 scopus 로고    scopus 로고
    • Use of Lorenz curves and Gini coefficients to assess yield inequality within paddocks
    • Sadras V, Bongiovanni R, (2004) Use of Lorenz curves and Gini coefficients to assess yield inequality within paddocks. Field Crops Research 90: 303-310.
    • (2004) Field Crops Research , vol.90 , pp. 303-310
    • Sadras, V.1    Bongiovanni, R.2
  • 57
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L, (2001) Random forests. Mach learn 45: 5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 58
    • 79951527638 scopus 로고    scopus 로고
    • DROP: an SVM domain linker predictor trained with optimal features selected by random forest
    • Ebina T, Toh H, Kuroda Y, (2011) DROP: an SVM domain linker predictor trained with optimal features selected by random forest. Bioinformatics 27: 487-494.
    • (2011) Bioinformatics , vol.27 , pp. 487-494
    • Ebina, T.1    Toh, H.2    Kuroda, Y.3
  • 59
    • 0037432532 scopus 로고    scopus 로고
    • Structural location of disease-associated single-nucleotide polymorphisms
    • Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, et al. (2003) Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol 327: 1021-1030.
    • (2003) J Mol Biol , vol.327 , pp. 1021-1030
    • Stitziel, N.O.1    Tseng, Y.Y.2    Pervouchine, D.3    Goddeau, D.4    Kasif, S.5
  • 60
    • 13944277320 scopus 로고    scopus 로고
    • Prediction of protein B-factor profiles
    • Yuan Z, Bailey TL, Teasdale RD, (2005) Prediction of protein B-factor profiles. Proteins 58: 905-912.
    • (2005) Proteins , vol.58 , pp. 905-912
    • Yuan, Z.1    Bailey, T.L.2    Teasdale, R.D.3
  • 61
    • 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
  • 62
    • 80055062088 scopus 로고    scopus 로고
    • Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach
    • Wang XF, Chen Z, Wang C, Yan RX, Zhang Z, et al. (2011) Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach. PLoS One 6: e26767.
    • (2011) PLoS One , vol.6
    • Wang, X.F.1    Chen, Z.2    Wang, C.3    Yan, R.X.4    Zhang, Z.5
  • 63
    • 19544392545 scopus 로고    scopus 로고
    • Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
    • Bao L, Cui Y, (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics 21: 2185-2190.
    • (2005) Bioinformatics , vol.21 , pp. 2185-2190
    • Bao, L.1    Cui, Y.2
  • 64
    • 70350671733 scopus 로고    scopus 로고
    • Automated inference of molecular mechanisms of disease from amino acid substitutions
    • Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, et al. (2009) Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25: 2744-2750.
    • (2009) Bioinformatics , vol.25 , pp. 2744-2750
    • Li, B.1    Krishnan, V.G.2    Mort, M.E.3    Xin, F.4    Kamati, K.K.5
  • 65
    • 33845937432 scopus 로고    scopus 로고
    • Structure of ATP-bound human ATP:cobalamin adenosyltransferase
    • Schubert HL, Hill CP, (2006) Structure of ATP-bound human ATP:cobalamin adenosyltransferase. Biochemistry 45: 15188-15196.
    • (2006) Biochemistry , vol.45 , pp. 15188-15196
    • Schubert, H.L.1    Hill, C.P.2
  • 66
    • 15244361704 scopus 로고    scopus 로고
    • Genetic analysis of three genes causing isolated methylmalonic acidemia: identification of 21 novel allelic variants
    • Martínez MA, Rincón A, Desviat LR, Merinero B, Ugarte M, et al. (2005) Genetic analysis of three genes causing isolated methylmalonic acidemia: identification of 21 novel allelic variants. Mol Genet Metab 84: 317-325.
    • (2005) Mol Genet Metab , vol.84 , pp. 317-325
    • Martínez, M.A.1    Rincón, A.2    Desviat, L.R.3    Merinero, B.4    Ugarte, M.5
  • 67
    • 57649123149 scopus 로고    scopus 로고
    • Crystal structure of human plasma platelet-activating factor acetylhydrolase: structural implication to lipoprotein binding and catalysis
    • Samanta U, Bahnson BJ, (2008) Crystal structure of human plasma platelet-activating factor acetylhydrolase: structural implication to lipoprotein binding and catalysis. J Biol Chem 283: 31617-31624.
    • (2008) J Biol Chem , vol.283 , pp. 31617-31624
    • Samanta, U.1    Bahnson, B.J.2
  • 68
    • 0037069653 scopus 로고    scopus 로고
    • Structural basis of BMP signalling inhibition by the cystine knot protein Noggin
    • Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, et al. (2002) Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature 420: 636-642.
    • (2002) Nature , vol.420 , pp. 636-642
    • Groppe, J.1    Greenwald, J.2    Wiater, E.3    Rodriguez-Leon, J.4    Economides, A.N.5
  • 69
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede T, Kopp J, Guex N, Peitsch MC, (2003) SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 31: 3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 72
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.