id: 05549144
dt: a
an: 05549144
au: Jiménez-Montaño, Miguel A.; He, Matthew
ti: Irreplaceable amino acids and reduced alphabets in short-term and directed
    protein evolution.
so: Măndoiu, Ion (ed.) et al., Bioinformatics research and applications. 5th
    international symposium, ISBRA 2009, Fort Lauderdale, FL, USA, May
    13‒16, 2009. Proceedings. Berlin: Springer (ISBN
    978-3-642-01550-2/pbk). Lecture Notes in Computer Science 5542. Lecture
    Notes in Bioinformatics, 297-309 (2009).
py: 2009
pu: Berlin: Springer
la: EN
cc: 
ut: Codon volatility; amino acid changeability; genetic mutations; reduced
    alphabet
ci: 
li: doi:10.1007/978-3-642-01551-9_29
ab: Summary: In this paper we extend codon volatility definition to amino acid
    reduced alphabets to characterize mutations that conserve
    physical-chemical properties. We also define the average relative
    changeability of amino acids in terms of single-base codon
    self-substitution frequencies (identities). These frequencies are taken
    from an empirical codon substitution matrix [14]. It is shown that this
    index splits the amino acids into two groups: replaceable and
    irreplaceable. The same grouping is obtained from the size/complexity
    index introduced by Dufton [32]. Also, a 71 \% agreement is obtained
    with residues in mutually persistent conserved (MPC) positions [31].
    These positions play a key role in fold and functional determination.
    The residual 29 \% can be readily explained. 75 \% of residues with
    highest rank according to MPC positions have the highest probability of
    causing disease if mutated.
rv: