Big Chemical Encyclopedia

Chemical substances, components, reactions, process design ...

Articles Figures Tables About

Protein Context Features and Domains

Most amino acids play more than one structural or functional role, some of which could be distinguished by context in the sequence. For instance, the three types of Cys (S-S, free-SH, and ligand-SH) have very different conformational preferences and clustering [Pg.71]

Since the different domains often have quite different types of tertiary structure, they need to be described and classified separately and, if possible, should be predicted separately. Multiple domains should be considered for any sequence that suggests an internal repeat or that is longer than about 200 residues (250 for a/P structures or 100 for a disulfide-rich sequence). [Pg.72]

An effective measure of local context to predict protein local structures is the hydrophobic moment. The overall amphipathicity of any periodic structure has been quantitated in the hydrophobic moment. Even if the atomic coordinates of a protein are not known, the sequence hydrophobic moment can be estimated, as in [Pg.72]

The hydrophobicity profile is a simple way to quantify the concentration of hydrophobic residues along the linear polypeptide chain (Rose Dworkin, 1989). The construction of the profiles depends on the choice of the hydrophobicity scale and the window size. The profile is computed by averaging the hydrophobicity scales of amino acid residues within [Pg.72]

Another frequently used global information that covers protein context is the residue frequencies. The composition is often calibrated with that from the database as in Gamier et al. (1996), where only observed frequencies of amino acids and amino acid pairs are used for protein secondary structure prediction. [Pg.73]


See other pages where Protein Context Features and Domains is mentioned: [Pg.71]   


SEARCH



Domains context

Domains protein

© 2024 chempedia.info