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Volumn 32, Issue 4, 2011, Pages 358-368

Performance of mutation pathogenicity prediction methods on missense variants

Author keywords

Bioinformatics; Method evaluation; Pathogenicity prediction; SNPs

Indexed keywords

AMINO ACID;

EID: 79952764520     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21445     Document Type: Article
Times cited : (443)

References (62)
  • 2
    • 1542400269 scopus 로고    scopus 로고
    • Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
    • Ahmad S, Gromiha MM, Sarai A. 2004. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 20:477-486.
    • (2004) Bioinformatics , vol.20 , pp. 477-486
    • Ahmad, S.1    Gromiha, M.M.2    Sarai, A.3
  • 5
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45-48.
    • (2000) Nucleic Acids Res , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 6
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • Baldi P, Brunak S, Chauvin Y, Andersen CA F, Nielsen H. 2000. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16:412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen CA, F.4    Nielsen, H.5
  • 7
    • 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
  • 8
    • 44349130366 scopus 로고    scopus 로고
    • Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers
    • Barenboim M, Masso M, Vaisman, II, Jamison DC. 2008. Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers. Proteins 71:1930-1939.
    • (2008) Proteins , vol.71 , pp. 1930-1939
    • Barenboim, M.1    Masso, M.2    Vaisman, I.I.3    Jamison, D.C.4
  • 10
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: predict effect of non-synonymous polymorphisms on function
    • Bromberg Y, Rost B. 2007. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 35:3823-3835.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 11
    • 67749137351 scopus 로고    scopus 로고
    • Functional annotations improve the predictive score of human disease-related mutations in proteins
    • Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. 2009. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat 30:1237-1244.
    • (2009) Hum Mutat , vol.30 , pp. 1237-1244
    • Calabrese, R.1    Capriotti, E.2    Fariselli, P.3    Martelli, P.L.4    Casadio, R.5
  • 12
    • 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
  • 13
    • 23144461249 scopus 로고    scopus 로고
    • I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
    • Capriotti E, Fariselli P, Casadio R. 2005. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33:W306-W310.
    • (2005) Nucleic Acids Res , vol.33
    • Capriotti, E.1    Fariselli, P.2    Casadio, R.3
  • 15
    • 0015987426 scopus 로고
    • Prediction of protein conformation
    • Chou PY, Fasman GD. 1974. Prediction of protein conformation. Biochemistry 13:222-245.
    • (1974) Biochemistry , vol.13 , pp. 222-245
    • Chou, P.Y.1    Fasman, G.D.2
  • 16
    • 33847215114 scopus 로고    scopus 로고
    • Intrinsic disorder and protein modifications: building an SVM predictor for methylation. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB
    • Daily KM, Radivojac P., Dunker AK. 2005. Intrinsic disorder and protein modifications: building an SVM predictor for methylation. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB: 475-481.
    • (2005) , pp. 475-481
    • Daily, K.M.1    Radivojac, P.2    Dunker, A.K.3
  • 17
    • 0035999986 scopus 로고    scopus 로고
    • An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
    • Delorenzi M, Speed T. 2002. An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics 18:617-625.
    • (2002) Bioinformatics , vol.18 , pp. 617-625
    • Delorenzi, M.1    Speed, T.2
  • 20
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. 1995. Knowledge-based protein secondary structure assignment. Proteins 23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 23
    • 0034068308 scopus 로고    scopus 로고
    • Strategies in complex disease mapping
    • Johnson GC, Todd JA. 2000. Strategies in complex disease mapping. Curr Opin Genet Dev 10:330-334.
    • (2000) Curr Opin Genet Dev , vol.10 , pp. 330-334
    • Johnson, G.C.1    Todd, J.A.2
  • 24
    • 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
  • 25
    • 60749104999 scopus 로고    scopus 로고
    • Next generation tools for the annotation of human SNPs
    • Karchin R. 2009. Next generation tools for the annotation of human SNPs. Brief Bioinform 10:35-52.
    • (2009) Brief Bioinform , vol.10 , pp. 35-52
    • Karchin, R.1
  • 28
    • 34848835086 scopus 로고    scopus 로고
    • Spectrum of disease-causing mutations in protein secondary structures
    • Khan S, Vihinen M. 2007. Spectrum of disease-causing mutations in protein secondary structures. BMC Struct Biol 7:56.
    • (2007) BMC Struct Biol , vol.7 , pp. 56
    • Khan, S.1    Vihinen, M.2
  • 29
    • 77952706843 scopus 로고    scopus 로고
    • Performance of protein stability predictors
    • Khan S, Vihinen M. 2010. Performance of protein stability predictors. Hum Mutat 31:675-684.
    • (2010) Hum Mutat , vol.31 , pp. 675-684
    • Khan, S.1    Vihinen, M.2
  • 30
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 32
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas A, Van Dyke M, Stock J. 1991. Predicting coiled coils from protein sequences. Science 252:1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 33
    • 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 405:442-451.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 34
    • 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
  • 35
    • 17244367767 scopus 로고    scopus 로고
    • Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
    • Mooney S. 2005. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform 6:44-56.
    • (2005) Brief Bioinform , vol.6 , pp. 44-56
    • Mooney, S.1
  • 37
    • 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
  • 38
    • 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
  • 39
    • 33750353461 scopus 로고    scopus 로고
    • Predicting the effects of amino acid substitutions on protein function
    • Ng PC, Henikoff S. 2006. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7:61-80.
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 61-80
    • Ng, P.C.1    Henikoff, S.2
  • 40
    • 0033670313 scopus 로고    scopus 로고
    • PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane
    • Ng PC, Henikoff JG, Henikoff S. 2000. PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics 16:760-766.
    • (2000) Bioinformatics , vol.16 , pp. 760-766
    • Ng, P.C.1    Henikoff, J.G.2    Henikoff, S.3
  • 41
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H, Engelbrecht J, Brunak S, von Heijne G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10:1-6.
    • (1997) Protein Eng , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    von Heijne, G.4
  • 44
    • 33751011339 scopus 로고    scopus 로고
    • Immunodeficiency mutation databases (IDbases)
    • Piirilä H, Väliaho J, Vihinen M. 2006. Immunodeficiency mutation databases (IDbases). Hum Mutat 27:1200-1208.
    • (2006) Hum Mutat , vol.27 , pp. 1200-1208
    • Piirilä, H.1    Väliaho, J.2    Vihinen, M.3
  • 48
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: server and survey
    • Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-3900.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3894-3900
    • Ramensky, V.1    Bork, P.2    Sunyaev, S.3
  • 50
    • 0029889988 scopus 로고    scopus 로고
    • PHD: predicting one-dimensional protein structure by profile-based neural networks
    • Rost B. 1996. PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol 266:525-539.
    • (1996) Methods Enzymol , vol.266 , pp. 525-539
    • Rost, B.1
  • 51
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B, Sander C. 1994. Conservation and prediction of solvent accessibility in protein families. Proteins 20:216-226.
    • (1994) Proteins , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 52
    • 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
  • 53
    • 33645288849 scopus 로고    scopus 로고
    • PROFbval: predict flexible and rigid residues in proteins
    • Schlessinger A, Yachdav G, Rost B. 2006. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics 22:891-893.
    • (2006) Bioinformatics , vol.22 , pp. 891-893
    • Schlessinger, A.1    Yachdav, G.2    Rost, B.3
  • 54
    • 2942689385 scopus 로고    scopus 로고
    • Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain
    • Shen B, Vihinen M. 2004. Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain. Protein Eng Des Sel 17:267-276.
    • (2004) Protein Eng Des Sel , vol.17 , pp. 267-276
    • Shen, B.1    Vihinen, M.2
  • 59
    • 65649108490 scopus 로고    scopus 로고
    • Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods
    • Thusberg J, Vihinen M. 2009. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum Mutat 30:703-714.
    • (2009) Hum Mutat , vol.30 , pp. 703-714
    • Thusberg, J.1    Vihinen, M.2
  • 61
    • 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, Gasteiger E, Bairoch A. 2004. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat 23:464-470.
    • (2004) Hum Mutat , vol.23 , pp. 464-470
    • Yip, Y.L.1    Scheib, H.2    Diemand, A.V.3    Gattiker, A.4    Famiglietti, L.M.5    Gasteiger, E.6    Bairoch, A.7
  • 62
    • 33645764714 scopus 로고    scopus 로고
    • SNPs3D: candidate gene and SNP selection for association studies
    • Yue P, Melamud E, Moult J. 2006. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 7:166.
    • (2006) BMC Bioinformatics , vol.7 , pp. 166
    • Yue, P.1    Melamud, E.2    Moult, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.