Evaluation of structural and evolutionary contributions to deleterious mutation prediction

Journal of Molecular Biology

Volumn 322, Issue 4, 2002, Pages 891-901

  Saunders, Christopher T ^a   Baker, David ^b,c  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Deleterious mutation prediction; Human disease allele; Protein evolution; Protein mutagenesis; Protein structure prediction

Indexed keywords

PROTEIN;

AB INITIO CALCULATION; ACCURACY; ALLELE; ARTICLE; MOLECULAR EVOLUTION; MUTAGENESIS; MUTATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0036387236     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00813-6     Document Type: Article

References (25)

1. Ng, P. C. & Henikoff, S. (2001). Predicting deleterious amino acid substitutions. Genome Res. 11, 863-874.
2. Sunyaev, S., Ramensky, V., Koch, I., Lathe, W. C., III, Kondrashov, A. S. & Bork, P. (2001). Prediction of deleterious human alleles. Hum. Mol. Genet. 10, 591-597.
3. Wang, Z. & Moult, J. (2001). SNP's, protein structure, and disease. Hum. Mut. 17, 263-270.
4. Lichtarge, O., Bourne, H. R. & Cohen, F. E. (1996). An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257, 342-358.
5. Markiewicz, P., Kleina, L., Cruz, C., Ehret, S. & 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.
6. Loeb, D. D., Swanstrom, R., Everitt, L., Manchester, M., Stamper, S. E. & Hutchison, C. A., III (1989). Complete mutagenesis of the HIV-1 protease. Nature, 340, 397-400.
7. Rennell, D., Bouvier, S. E., Hardy, L. W. & Poteete, A. R. (1991). Systematic mutation of bacteriophage T4 lysozyme. J. Mol. Biol. 222, 67-87.
8. Bairoch, A. & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28, 45-48.
9. Chasman, D. & 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.
10. Henikoff, S. & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. 89, 10915-10919.
11. Voigt, C. A., Mayo, S. L., Arnold, F. H. & Wang, Z. (2001). Computational method to reduce the search space for directed protein evolution. Proc. Natl Acad. Sci. 98, 3778-3783.
12. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
13. Simons, K. T., Strauss, C. & Baker, D. (2001). Prospects for ab initio protein structural genomics. J. Mol. Biol. 306, 1191-1199.
14. Fischer, D. & Eisenberg, D. (1996). Protein fold recognition using sequence-derived predictions. Protein Sci. 5, 947-955.
15. Panchenko, A., Marchler-Bauer, A. & Bryant, S. H. (1999). Threading with explicit models for evolutionary conservation of structure and sequence. Proteins: Struct. Funct. Genet. 37, 133-140.
16. Murzin, A. (1999). Structure classification-based assessment of CASP3 predictions for the fold recognition targets. Proteins: Struct. Funct. Genet, 37, 88-103.
17. Panchenko, A. R., Marchler-Bauer, A. & Bryant, S. H. (2000). Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol. 296, 1319-1331.
18. Tatusov, R. L., Altschul, S. F. & Koonin, E. V. (1994). Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. 91, 12091-12095.
19. Henikoff, S. & Henikoff, J. G. (1991). Automated assembly of protein blocks for database searching. Nucl. Acids Res. 19, 6565-6572.
20. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). GappedBLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
21. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H. et al. (2000). The Protein Data Bank. Nucl. Acids Res. 28, 235-242.
22. Rost, B. & Sander, C. (1994). Conservation and prediction of solvent accessibility in protein families. Proteins: Struct. Funct. Genet. 20, 216-226.
23. Hobohm, U., Scharf, M. & Schneider, R. (1993). Selection of representative protein data sets. Protein Sci. 1, 409-417.
24. Breiman, L., Friedman, J. H., Olshen, R. A. & Stone, C. J. (1984). Classification and Regression Trees, pp. 59-129, Wadsworth, Pacific Grove, CA.
25. Therneau, T. M. & Atkinson, E. J. (1997). An introduction to recursive partitioning using the RPART routines, Technical Report Series No. 61, pp. 5-13, Department of Health Science Research, Mayo Clinic, Rochester, MN, http://www.mayo.edu/hsr/ techrpt.html