Predicting protein stability changes from sequences using support vector machines

Bioinformatics

Volumn 21, Issue SUPPL. 2, 2005, Pages

  Capriotti, Emidio ^a   Fariselli, Piero ^a   Calabrese, Remo ^a   Casadio, Rita ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CORRELATION ANALYSIS; ENERGY BALANCE; GENE MUTATION; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN STABILITY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURAL PROTEOMICS; THERMODYNAMICS;

EID: 27544469800     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1109     Document Type: Article

References (19)

1. Apetri,A.C. et al. (2004) The effect of disease-associated mutations on the folding pathway of human prion protein. J. Biol. Chem., 279, 31048-31052.
2. Bava,K.A. et al. (2004) ProTherm, version 4.0: Thermodynamic database for proteins and mutants. Nucleic Acids Res., 32, D120-D121.
3. Calzolai,L. et al. (2000) NMR structures of three single-residue variants of the human prion protein. Proc. Natl Acad. Sci. USA, 97, 8340-8345.
4. Capriotti,E. et al. (2004) A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics, 20 (suppl. 1), I63-I68.
5. Daggett,V. and Fersht A.R. (2003) Is there a unifying mechanism for protein folding? Trends Biochem, Sci., 28, 18-25.
6. Dobson,C.M. (2003) Protein folding and misfolding. Nature, 426, 884-890.
7. Funahashi,J. et al. (2001) Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins? Protein Eng., 14, 127-134.
8. Gilis,D. and Rooman,M. (1997) Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol., 272, 276-290.
9. Guerois,R. et al. (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol., 320, 369-387.
10. Kwasigroch,J.M. et al. (2002) PoPMuSiC, rationally designing point mutations in protein structures. Bioinformatics, 18, 1701-1702.
11. Liemann,S. and Glockshuber,R. (1999) Influence of amino acid substitutions related to inherited human prion diseases on the thermodynamic stability of the cellular prion protein, Biochemistry, 38, 3258-3267.
12. Pitera,J.W. and Kollman,P.A. (2000) Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins, 41, 385-397.
13. Prevost,M. et al. (1991) Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the Ile-96-Ala mutation in barnase. Proc. Natl Acad. Sci. USA, 88, 10880-10884.
14. Shnyrov,V.L. et al. (2000) Comparative calorimetric study of non-amyloidogenic and amyloidogenic variants of the homotetrameric protein transthyretin. Biophys. Chem., 88, 61-67.
15. Selkoe,D.J. (2003) Folding proteins in fatal ways. Nature, 426, 900-904.
16. Topham,C.M. et al. (1997) Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. Protein Eng., 10, 7-21.
17. Wang,Z. and Moult,J. (2001) SNPs, protein structure, and disease. Hum. Mutat., 17, 263-270.
18. Wang,Z. and Moult,J. (2003) Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor Vbeta domain. Proteins, 53, 748-757.
19. Zhou,H. and Zhou,Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.