Protein Secondary Structure

Protein secondary structure (SS) is the general three-dimensional form of local segments of proteins.

Secondary structure can be formally defined by the pattern of hydrogen bonds of the protein

(such as alpha helices and beta sheets) that are observed in an atomic-resolution structure.

More specifically, the secondary structure is defined by the patterns of hydrogen bonds formed between

amine hydrogen (-NH) and carbonyl oxygen (C=O) atoms contained in the backbone peptide bonds of the protein.


For more info see the Wikipedia article on [protein secondary structure]

(https://en.wikipedia.org/wiki/Protein_secondary_structure).

There are various ways to obtain the SS annotation of a protein structure:

- **Authors assignment**: the authors of the structure describe the SS, usually identifying helices

and beta-sheets, and they assign the corresponding type to each residue involved. The authors assignment

can be found in the `PDB` and `mmCIF` file formats deposited in the PDB, and it can be parsed in **BioJava**

when a `Structure` is loaded.

- **Prediction from Atom coordinates**: there exist various programs to predict the SS of a protein.

The algorithms use the atom coordinates of the aminoacids to detemine hydrogen bonds and geometrical patterns

that define the different types of protein secondary structure. One of the first and most popular algorithms

is `DSSP` (Dictionary of Secondary Structure of Proteins). **BioJava** has an implementation of the algorithm,

written originally in C++, which will be described in the next section.

- **Prediction from sequence**: Other algorithms use only the aminoacid sequence (primary structure) of the protein,

nd predict the SS using the SS propensities of each aminoacid and multiple alignments with homologous sequences

(i.e. [PSIPRED](http://bioinf.cs.ucl.ac.uk/psipred/)). At the moment **BioJava** does not have an implementation

of this type, which would be more suitable for the sequence and alignment modules.

Following the `DSSP` convention, **BioJava** defines 8 types of secondary structure:

E = extended strand, participates in β ladder

B = residue in isolated β-bridge

H = α-helix

G = 3-helix (3-10 helix)

I = 5-helix (π-helix)

T = hydrogen bonded turn

S = bend

_ = loop (any other type)

The algorithm implemented in BioJava for the prediction of SS is `DSSP`. It is described in the paper from

[Kabsch W. & Sander C. in 1983](http://onlinelibrary.wiley.com/doi/10.1002/bip.360221211/abstract)

[](http://www.ncbi.nlm.nih.gov/pubmed/6667333).