From amino acid sequences

Different side chains have been found to have weak but definite preferences either for or against being in a helices. Thus Ala (A), Glu (E), Leu (L), and Met (M) are good a-helix formers, while Pro (P), Gly (G), Tyr (Y), and Ser (S) are very poor. Such preferences were central to all early attempts to predict secondary structure from amino acid sequence, but they are not strong enough to give accurate predictions. 

Since the outside of the barrel faces hydrophobic lipids of the membrane and the inside forms the solvent-exposed channel, one would expect the P strands to contain alternating hydrophobic and hydrophilic side chains. This requirement is not strict, however, because internal residues can be hydrophobic if they are in contact with hydrophobic residues from loop regions. The prediction of transmembrane p strands from amino acid sequences is therefore more difficult and less reliable than the prediction of transmembrane a helices. 

Transmembrane a helices can be predicted from amino acid sequences... 

Ahmad, S., Gromiha, M.M., and Sarai, A. (2003) Real value prediction of solvent accessibility from amino acid sequence. Proteins 50(4), 629-635. 

Currently, there exists an enormous and growing deficit between the number of polypeptides whose amino acid sequence has been determined and the numbers of polypeptides whose three-dimensional structure has been resolved. Given the complexities of resolving three-dimensional structure experimentally, it is not surprising that scientists are continually attempting to develop methods by which they could predict higher order structure from amino acid sequence data. Although modestly successful secondary structure predictive approaches have been developed, no method by which tertiary structure may be predicted from primary data has thus far been developed. 

Ganesh, C., N. Eswar, S. Srivastava, C. Ramakrishnan, and R. Varadarajan. 1999. Prediction of the maximal stability temperature of monomeric globular proteins solely from amino acid sequence. FEBS Lett 454 31-36. 

Table Vm. Structural Interpretations Deduced From Amino Acid Sequence Computer Analysis of the Thermoanaerobacter Strain B6A Endoxylanase Gene...

Hopp TP, Woods KR. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A78, 3824-8. 

FIGURE 3-33 Evolutionary tree derived from amino acid sequence comparisons. A bacterial evolutionary tree, based on the sequence divergence observed in the GroEL family of proteins. Also included in this tree (lower right) are the chioropiasts (chi.) of some nonbacteriai species. 

Figure 13.3. The Tree View is used to draw a phylogenetic tree from treefile of Phylip in radial, slanted cladogram, rectangular cladogram, or phytogram. The rectangular dado-gram for treefile derived from amino acid sequences of ribonucleases is drawn with TreeView.

Aalberse, R. C. and Stadler, B. M. 2006. In silico predictability of allergenicity From amino acid sequence via 3-D structure to allergenicity. Mol Nutr Food Res 50(7) 625-627. 

Gill, S.C. and von Hippel, P.H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry 182,319-326. Erratum in Analytical Biochememistry 1990, 189,283. 

Fig. 4.22. Design of a possible functional primer sequence from amino-acid sequence data. (Houghton et a .. 1980.)...

Peitsch, M. C. (1995) Protein modeling by E-mail. From amino acid sequence to protein structure a free one-hour service. Bio/Technol. 13, 658-660. 

Fig. 4-12 Phylogenetic tree constructed from amino acid sequences of cytochrome c.

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