SNAP: Predict effect of non-synonymous polymorphisms on function

Nucleic Acids Research

Volumn 35, Issue 11, 2007, Pages 3823-3835

  Bromberg, Yana ^a   Rost, Burkhard ^a,b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b NorthEast Structural Genomics Consortium (NESG)   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; ARTIFICIAL NEURAL NETWORK; CALIBRATION; COMPUTER ANALYSIS; COMPUTER MODEL; GENETIC POLYMORPHISM; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; RELIABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; CHEMISTRY; GENETIC DISORDER; GENETICS; HUMAN; METABOLISM; METHODOLOGY; PROTEIN CONFORMATION; REPRODUCIBILITY; SEQUENCE ANALYSIS; VALIDATION STUDY;

NON-A, NON-B HEPATITIS VIRUS;

PROTEIN;

AMINO ACID SUBSTITUTION; COMPUTATIONAL BIOLOGY; GENETIC DISEASES, INBORN; HUMANS; NEURAL NETWORKS (COMPUTER); POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN;

EID: 34547100092     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm238     Document Type: Article

References (59)

1. Kawabata,T., Ota,M. and Nishikawa,K. (1999) The protein mutant database. Nucleic Acids Res., 27, 355-357.
2. Nishikawa,K., Ishino,S., Takenaka,H., Norioka,N., Hirai,T., Yao,T. and Seto,Y. (1994) Constructing a protein mutant database. Protein Eng. 7, 773.
3. Sunyaev,S.R., Eisenhaber,F., Rodchenkov,I.V., Eisenhaber,B., Tumanyan,V.G. and Kuznetsov,E.N. (1999) PSIC: Profile extraction from sequence alighnments with position-specific counts of independent observations. Protein Eng., 12, 387-394.
4. Chakravarti,A. (2001) To a future of genetic medicine. Nature, 409, 822-823.
5. The FANTOM Consortium, Carninci,P., Kasukawa,T., Katayama,S., Gough.J., Frith,M.C., Maeda,N., Oyama,R., Ravasi,T et al. (2005) The Transcriptional landscape of the mammalian genome. Science, 309 1559-1563.
6. Liu,J., Gough,J. and Rost,B. (2006) Distinguishing protein-coding from non-coding RNA through support vector machines. PLoS Genet., 2 e29;DOI: 10.1371/journal.pgen.0020029.
7. Ng,P.C. and Henikoff,S. (2006) Predicting the effects of amino Acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet. 7, 61-80.
8. Wishner,B.C., Ward,K.B., Lathman,E.E. and Love,W.E. (1975) Crystal structure of sickle-cell deoxyhemoglobin at 5A resolution. J. Mol. Biol., 98, 179-194.
9. Kovacs,P., Stumvoll,M., Bogardus,C., Hanson,R.L. and Baier,L.J. (2006) A functional Tyr1306Cys variant in LARG is associated with increased insulin action in vivo. Diabetes, 55, 1497-1503.
10. Wang,Z. and Moult,J. (2001) SNPs, protein structure and disease. Hum. Mutat., 17, 263-270.
11. Chasman,D. and Adams,R.M. (2001) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure based assessment of amino acid variation. J. Mol. Biol., 307, 683-706.
12. Ng,P.C. and Henikoff,S. (2001) Predicting deleterious amino acid substitutions. Genome Res., 11, 863-874.
13. Ng,P.C. and Henikoff,S. (2002) Accounting for human polymorphisms predicted to affect protein function. Genome Res., 12, 436-446.
14. Ng,P.C. and Henikoff,S. (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res., 31, 3812-3814.
15. Ramensky,V., Bork,P. and Sunyaev,S.R. (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res., 30, 3894-3900.
16. Saunders,C.T. and Baker,D. (2002) Evaluation of structural and evolutionary contributions to deleterious mutations prediction. J. Mol. Biol., 322, 891-901.
17. Yue,P., Li,Z. and Moult,J. (2005) Loss of protein structure stability as a major causative factor in monogenic disease. J. Mol. Biol., 353, 459-463.
18. Ferrer-Costa,C., Orozco,M. and de la Cruz,X. (2004) Sequence-based prediction of pathological mutations. Proteins, 57, 811-819.
19. Clifford,R.J., Edmonson,M.N., Nguyen,C., Scherpbier,T., Hu,Y. and Buetow,K.H. (2004) Bioinformatics tools for single nucleotide polymorphism discovery and analysis. Ann. NY Acad. Sci., 1020 101-109.
20. Verzilli,C.J., John, C.Whittaker., Stallard,N. and Chasman,D. (2005) A hierarchical bayesian model for predicting the functional consequences of amino-acid polymorphisms. Appl. Statist., 54, 191-206.
21. Krishnan,V.G. and Westhead,D.R. (2003) A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function. Bioinformatics, 19, 2199-2209.
22. Capriotti,E., Fariselli,P. and Casadio,R. (2004) A neural network-based method for predicting protein stability changes upon single point mutation. Bioinformatics, 1, 1-6.
23. Bao,L. and Cui,Y. (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics, 21, 2185-2190.
24. Cohen,J.C., Kiss,R.S., Pertsemlidis,A., Marcel,Y.L., McPherson,R. and Hobbs,H.H. (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science, 305, 869-872.
25. Letourneau,I.J., Deeley,R.G. and Cole,S.P. (2005) Functional characterization of non-synonymous single nucleotide polymorphisms in the gene encoding human multidrug resistance protein 1 (MRP1/ABCC1). Pharmacogenet. Genomics, 15, 647-657.
26. Freimuth,R.R., Xiao,M., Marsh,S., Minton,M., Addleman,N., Van Booven,D.J., McLeod,H.L. and Kwok,P.Y. (2005) Polymorphism discovery in 51 chemotherapy pathway genes. Hum. Mol. Genet., 14, 3595-3603.
27. Sunyaev,S.R., Ramensky,V., Koch,I., Lathe,W.I., Kondrashov,A.S. and Bork,P. (2001) Prediction of deleterious human alleles. Hum. Mol. Genet., 10, 591-597.
28. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
29. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Capped Blast and PSI-Blast: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
30. Sander,C. and Schneider,R. (1991) Database of homology-derived structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
31. Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
32. Markiewicz,P., Kleina,L.G., Cruz,C., Ehret,S. and Miller,J.H. (1994) Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as 'spacers' which do not require a specific sequence. J. Mol. Biol., 240, 421-433.
33. Rennel,D., Bouvier,S.E., Hardy,L.W. and Poteete,A.R. (1991) Systematic mutations of bacteriophage T4 lysozyme. J. Mol. Biol., 222, 67-88.
34. Loeb,D.D., Swanstrom,R., Everitt,L., Manchester,M., Stamper,S.E. and Hutchison,C.A. (1989) Complete mutagenesis of the HIV-1 protease. Nature, 340, 397-400.
35. Rost,B. (2005). In Walker,J.E. (ed.), The Proteomics Protocols Handbook, Humana, Totowa, NJ, pp. 875-901.
36. Rost,B. (1996) PHD: Predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol., 266, 525-539.
37. Rost,B. and Sander,C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
38. Joachims,T. (1999). In Schölkopf,B., Burges,C. and Smola,A. (eds), Advances in Kernel Methods - Support Vector Learning, MIT-Press, Cambridge, MA.
39. Ofran,Y. and Rost,B. (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Lett., 544, 236-239.
40. Nair,R. and Rost,B. (2005) Mimicking cellular sorting improves prediction of subcellular localization. J. Mol. Biol., 348, 85-100.
41. Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger.E., Huang,H. et al. (2006) The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.
42. Apweiler,R., Bairoch,A., Wu,C.H., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. et al. (2004) UniProt: The universal protein knowledgebase. Nucleic Acids Res., 32, D115-D119.
43. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
44. Bairoch,A., Apweiler,R., Wu,C.H., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
45. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
46. Rost,B. and Sander,C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins Struct. Funct. Genet., 20, 216-226.
47. Rost,B. (2005) How to use protein ID structure predicted by PROFphd. In Walker, J. E. (ed.), The Proteomics Protocols Handbook. Humana, Totowa NJ, pp. 875-901.
48. Schlessinger,A., Yachdav,G. and Rost,B. (2006) PROFbval: Predict flexible and rigid residues in proteins. Bioinformatics, 22, 891-893.
49. Bateman,A., Lachlan,C., Durbin,R., Finn,R.D.,. Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M. et al. (2004) The Pfam Protein Families Database. Nucleic Acids Res., 32, D138-D141.
50. Ng,P.C., Henikoff,J.G. and Henikoff,S. (2000) PHAT: A transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics, 16, 760-766.
51. Fu,L. (1994) Neural Networks in Computer Intelligence 1st edn. McGraw-Hill Inc., New York, NY, USA.
52. Efron,B., Halloran,E. and Holmes,S. (1996) Bootstrap confidence levels for phylogenetic trees. Proc. Natl Acad. Sci. USA, 93, 13429-13434.
53. Yeo,G.S., Lank,E.J., Farooqi,I.S., Keogh,J., Challis,B.G. and O'Rahilly,S. (2003) Mutations in the human melanocortin-4 receptor gene associated with severe familial obesity disrupts receptor function through multiple molecular mechanisms. Hum. Mol. Genet., 12, 561-574.
54. Ofran,Y. and Rost,B. (2007) ISIS: Interaction sites identified from sequence. Bioinformatics, 23, e13-6.
55. Rost,B. (2001) Review: Protein secondary structure prediction continues to rise. J. Struct Biol, 134, 204-218.
56. Punta,M. and Rost,B. (2005) PROFcon: Novel prediction of long-range contacts. Bioinformatics, 21, 2960-2968.
57. Schlessinger,A. and Rost,B. (2005) Protein flexibility and rigidity predicted from sequence. Proteins Struct. Funct. Bioinform., 61 115-126.
58. Kidokoro,S., Miki,Y., Endo,K., Wada,A., Nagao,H., Miyake,T., Aoyama,A., Yoneya,T., Kai,K. et al. (1995) Remarkable activity enhancement of thermolysin mutants. FEBS Lett., 367, 73-76.
59. Govaerts,C., Srinivasan,S., Shapiro,A., Zhang,S., Picard,F., Clement,K., Lubrano-Berthelier,C. and Vaisse,C. (2005) Obesity-associated mutations in the melanocortin 4 receptor provide novel insights into its function. Peptides, 26, 1909-1919.