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Conservation Score 寫法

Link

Conservation scores of residues

Conservation of residues is identified by comparing the sequence of PDB (14) entries with sequences deposited in Swiss-Prot (15) using a local implementation of the public server ConSurf (10) (http://consurf.tau.ac.il). The ClustalW (17) aligned homologous sequences found by PSI-BLAST (19) are used to calculate the measure of conservation by the Rate4Site algorithm (20). Residues are classified into nine categories according to their real conservation score. A score of 1 represents the most variable residues and a score of 9 represents the most conservative ones.

In our study of TIM-barrel proteins (11), we have used the following conditions to predict the SRs: (i) H_P ≥ 20 kcal/mol; (ii) LRO ≥ 0.02; (iii) SC ≥ 1; and (iv) conservation score ≥ 6.

Surrounding hydrophobicity

The experimental values are given below:

Ala     Asp    Cys    Glu    Phe    Gly     His     Ile    Lys    Leu    Met    Asn       
0.87   0.66   1.52   0.67   2.87   0.10   0.87   3.15  1.64   2.17  1.67   0.09    

Pro    Gln    Arg    Ser    Thr    Val     Trp     Tyr
2.77   0.00   0.85  0.07   0.07  1.87   3.77   2.67



Form

1. Book ( Google book)

    Protein Bioinformatics From Sequence to Function



2. Papers:  Nature 1978   Manavalan