Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment

Bioinformatics

Volumn 25, Issue 11, 2009, Pages 1356-1362

  Peterson, Eric L ^a   Kondev, Jané ^b   Theriot, Julie A ^c   Phillips, Rob ^a  

^a California Institute of Technology   (United States)

^b BRANDEIS UNIVERSITY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; INFORMATION RETRIEVAL; MOLECULAR RECOGNITION; PATTERN RECOGNITION; PRIORITY JOURNAL; PROTEIN FOLDING; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 65649149743     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp164     Document Type: Article

References (40)

1. Abkevich,V.I. and Shakhnovich,E.I. (2000) What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis.J. Mol. Biol., 300, 975-985.
2. Andersen,C.A.F. and Brunak,S. (2004) Representation of protein-sequence information by amino acid subalphabets. AI Mag, 25, 97-104.
3. Benson,S.D. et al. (2004) Does common architecture reveal a viral lineage spanning all three domains of life? Mol. Cell, 16, 673-85.
4. Bork,P. and Grunwald,C. (1990) Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach. Eur. J. Biochem., 191, 347-358.
5. Bork,P. et al. (1992) An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shockproteins. Proc. Natl Acad. Sci. USA, 89, 7290-7294.
6. Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
7. Cieplak,M. et al. (2001) Amino acid classes and the protein folding problem. J. Chem. Phys., 114, 1420-1423.
8. Dietmann,S. et al. (2001) A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res., 29, 55-57.
9. Dill,K.A. (1985) Theory for the folding and stability of globular proteins. Biochemistry, 24, 1501-1509.
10. Fan,K. and Wang,W. (2003) What is the minimum number of letters required to fold a protein? J. Mol. Biol., 328, 921-926.
11. Grant,A. et al. (2004) Progress towards mapping the universe of protein folds. Genome Biol., 5, 107.
12. Green,R.E. and Brenner,S.E. (2002) Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proc. IEEE, 90, 1834-1847.
13. Hanley,J.A. and McNeil,B.J. (1982) The meaning and use of the area under a Receiver Operating Characteristic (ROC) curve. Radiology, 143 29-36.
14. Hecht,M.H. et al. (2004) De novo proteins from designed combinatorial libraries. Protein Sci., 13, 1711-1723.
15. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
16. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
17. Holm,L. and Sander,C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88-96.
18. Johnson,M.S. and Overington,J.P. (1993) A structural basis for sequence comparisons. An evaluation of scoring methodologies. J. Mol. Biol. 233, 716-738.
19. Landes,C. and Risler,J.L. (1994) Fast databank searching with a reduced amino-acid alphabet. Comput. Appl. Biosci., 10, 453-454.
20. Li,J. and Wang,W. (2007) Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids. Sci. China C Life Sci., 50, 392-402.
21. Li,H. et al. (1996) Emergence of preferred structures in a simple model of protein folding. Science, 273, 666-669.
22. Li,T. et al. (2003) Reduction of protein sequence complexity by residue grouping. Protein Eng., 16, 323-330.
23. Liu,X. et al. (2002) Simplified amino acid alphabets based on deviation of conditional probability from random background. Phys. Rev. E, 66, 021906.
24. Magliery,T.J. and Regan,L. (2004) A cell-based screen for function of the four-helix bundle protein Rop: A new tool for combinatorial experiments in biophysics. Protein Eng. Des. Sel., 17, 77-83.
25. Melo,F. and Marti-Renom,M.A. (2006) Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Proteins, 63, 986-995.
26. Mirny,L.A. and Shakhnovich,E.I. (1999) Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol., 291, 177-196.
27. Miyazawa,S. and Jernigan,R.L. (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol., 256, 623-644.
28. Munson,M. et al. (1994) Redesigning the hydrophobic core of a four-helix-bundle protein. Protein Sci., 3, 2015-2022.
29. Murphy,L.R. et al. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng. 13, 149-152.
30. Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
31. Pearson,W.R. (1991) Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 11, 635-650.
32. Price,G.A. et al. (2005) Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics, 21, 3824-3831.
33. Prlić,A. et al. (2000) Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng., 13 545-550.
34. Riddle,D.S. et al. (1997) Functional rapidly folding proteins from simplified amino acid sequences. Nat. Struct. Biol., 4, 805-809.
35. Schafmeister,C.E. et al. (1997) A designed four helix bundle protein with native-like structure. Nat. Struct. Biol., 4, 1039-1046.
36. Sjölander,K. et al. (1996) Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
37. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
38. Solis,A.D. and Rackovsky,S. (2000) Optimized representations and maximal information in proteins. Proteins, 38, 149-164.
39. Thomas,P.D. and Dill,K.A. (1996) An iterative method for extracting energy-like quantities from protein structures. Proc. Natl Acad. Sci. USA, 93, 11628-11633.
40. Wang,J. and Wang,W. (1999) A computational approach to simplifying the protein folding alphabet. Nat. Struct. Biol., 6, 1033-1038.