In
protein structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer ma ...
, STRIDE (Structural identification) is an
algorithm
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific Computational problem, problems or to perform a computation. Algorithms are used as specificat ...
for the assignment of
protein secondary structure
Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure ...
elements given the atomic coordinates of the protein, as defined by
X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
,
protein NMR Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and ...
, or another protein structure determination method. In addition to the
hydrogen bond
In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...
criteria used by the more common
DSSP algorithm, the STRIDE assignment criteria also include
dihedral angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the uni ...
potentials. As such, its criteria for defining individual secondary structures are more complex than those of DSSP. The STRIDE
energy function
Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfi ...
contains a hydrogen-bond term containing a
Lennard-Jones-like 8-6 distance-dependent potential and two angular dependence factors reflecting the
planar
Planar is an adjective meaning "relating to a plane (geometry)".
Planar may also refer to:
Science and technology
* Planar (computer graphics), computer graphics pixel information from several bitplanes
* Planar (transmission line technologies), ...
ity of the optimized hydrogen bond geometry. The criteria for individual secondary structural elements, which are divided into the same groups as those reported by DSSP, also contain statistical
probability
Probability is the branch of mathematics concerning numerical descriptions of how likely an Event (probability theory), event is to occur, or how likely it is that a proposition is true. The probability of an event is a number between 0 and ...
factors derived from empirical examinations of solved structures with visually assigned secondary structure elements extracted from the
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...
.
Although DSSP is the older method and continues to be the most commonly used, the original STRIDE definition reported it to give a more satisfactory structural assignment in at least 70% of cases. In particular, STRIDE was observed to correct for the propensity of DSSP to assign shorter secondary structures than would be assigned by an expert crystallographer, usually due to the minor local variations in structure that are most common near the termini of secondary structure elements.
[Frishman D, Argos P. (1995). Knowledge-based protein secondary structure assignment. ''Proteins'' 23(4):566-79. ] Using a sliding-window method to smooth variations in assignment of single terminal residues, current implementations of STRIDE and DSSP are reported to agree in up to 95.4% of cases.
[Martin J, * Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF. (2005). Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. ''BMC Struct Biol'' 5:17. ] Both STRIDE and DSSP, among other common secondary structure assignment methods, are believed to underpredict
pi helices.
[Fodje MN, Al-Karadaghi S. (2002). Occurrence, conformational features and amino acid propensities for the pi-helix. ''Protein Eng'' 15(5):353-8. {{PMID, 12034854]
See also
*
DSSP
References
External links
STRIDE- includes web interface, a print of the original STRIDE paper, and software documentation
Paper on the original webserver implementation
Protein structure