SNAP predicts effect of mutations on protein function

Bioinformatics

Volumn 24, Issue 20, 2008, Pages 2397-2398

  Bromberg, Yana ^a   Yachdav, Guy ^a   Rost, Burkhard ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SUBSTITUTION; ARTICLE; CLIENT SERVER APPLICATION; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC SCREENING; HUMAN; MUTATIONAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; RELIABILITY;

EID: 53749105617     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn435     Document Type: Article

References (24)

1. 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.
2. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
3. Bateman,A. et al. (2004) The Pfam Protein Families Database. Nucleic Acids Res., 32, D138-D141.
4. Bromberg,Y. and Rost,B. (2007) SNAP: Predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res., 35, 3823-3835.
5. Bromberg,Y. and Rost,B. (2008) Comprehensive in silico mutagenesis highlights functionally improtant residues in proteins. Bioinformatics, 24, i207-i212.
6. Cargill,M. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet., 22 231-238.
7. Chan,S.J. et al. (1987) A mutation in the B chain coding region is associated with impaired proinsulin conversion in a family with hyperproinsulinemia. Proc. Natl Acad. Sci. USA, 84, 2194-2197.
8. Halushka,M.K. et al. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet., 22, 239-247.
9. Kawabata,T. et al. (1999) The protein mutant database. Nucleic Acids Res., 27, 355-357.
10. Ng,P.C. and Henikoff,S. (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res., 31, 3812-3814.
11. 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.
12. Nishikawa,K. et al. (1994) Constructing a protein mutant database. Protein Eng., 7, 773.
13. Norrman,M. et al. (2007) Structural characterization of insulin NPH formulations. Eur. J. Pharm. Sci., 30, 414-423.
14. Petrey,D. and Honig,B. (2003) GRASP2: Visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol., 374, 492-509.
15. Pruitt,K.D. et al. (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
16. Rost,B. (2005) How to use protein 1D structure predicted by PROFphd. In Walker,J.E. (ed.) The Proteomics Protocols Handbook. Humana, Totowa, NJ, pp. 875-901.
17. Rost,B. and Eyrich,V. (2001) EVA: Large-scale analysis of secondary structure prediction. Proteins Struct. Funct. Genet., 45 (Suppl. 5), S192-S199.
18. Rost,B. and Sander,C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins Struct. Funct. Genet., 20, 216-226.
19. Rost,B. et al. (2004) The PredictProtein server. Nucleic Acids Res., 32, W321 W326.
20. Sakura,H. et al. (1986) Structurally abnormal insulin in a diabetic patient. Characterization of the mutant insulin A3 (Val----Leu) isolated from the pancreas. J. Clin. Invest., 78, 1666-1672.
21. Schlessinger,A. et al. (2006) PROFbval: Predict flexible and rigid residues in proteins. Bioinformatics, 22, 891-893.
22. Sherry,S.T. et al. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
23. Shoelson,S. et al. (1983) Identification of a mutant human insulin predicted to contain a serine-for-phenylalanine substitution. Proc. Natl Acad. Sci. USA, 80, 7390-7394.
24. Sunyaev,S.R. et al. (1999) PSIC: Profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng., 12, 387-394.