Protein Segment Finder
Encyclopedia
Protein segment finder, or PSF , is a search engine to quickly identify protein segments obeying a set of primary, secondary and tertiary structure
constraints in the PDB (Protein Data Bank
)
, secondary structure
, disulfide bonds, hydrogen bond
s, and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure
. PSF is publicly available online at http://ari.stanford.edu/psf
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
constraints in the PDB (Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
)
Description
Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioinformatics. To assist this task, a search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints was designed. The database contains information such as amino acid sequencePeptide sequence
Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain in peptides and proteins. The sequence is generally reported from the N-terminal end containing free amino group to the C-terminal end containing free carboxyl group...
, secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
, disulfide bonds, hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
s, and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
. PSF is publicly available online at http://ari.stanford.edu/psf