Secondary protein structure prediction

Secondary structure means?

In biochemistry and structural biology,secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA).
It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.



Protein Structure Prediction

-One of the most important goals pursued by bioinformatics and theoretical chemistry.

-Aim is to predict the three-dimensional structure of proteins from their amino acid sequences, sometimes including additional relevant information such as the structures of related proteins.

-It deals with the prediction of a protein’s tertiary structure from its primary structure.

-High importance in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).

Some Examples of predictions are:

-Ab initio protein modelling
(Ab initio protein modelling methods seek to build three-dimensional protein models "from scratch", i.e., based on physical principles rather than (directly) on previously solved structures.)

-Comparative protein modelling

o Homology modelling (based on the reasonable assumption that two homologous proteins will share very similar structures.)

oProtein threading (scans the amino acid sequence of an unknown structure against a database of solved structures)

-Side Chain geometry prediction.
(Even structure prediction methods that are reasonably accurate for the peptide backbone often get the orientation and packing of the amino acid side chains wrong.

Methods that specifically address the problem of predicting side chain geometry include dead-end elimination and the self-consistent mean field method. Both discretize the continuously varying dihedral angles that determine a side chain's orientation relative to the backbone into a set of rotamers with fixed dihedral angles. The methods then attempt to identify the set of rotamers that minimize the model's overall energy. Rotamers are the side chain conformations with low energy. Such methods are most useful for analyzing the protein's hydrophobic core, where side chains are more closely packed; they have more difficulty addressing the looser constraints and higher flexibility of surface residues.)