STRIDE (protein)
Encyclopedia
In 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...

, STRIDE (Structural identification) is an algorithm
Algorithm
In mathematics and computer science, an algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning...

 for the assignment of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 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...

 elements given the atomic coordinates of the protein, as defined by X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...

, protein NMR, or another protein structure determination method. In addition to the 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...

 criteria used by the more common DSSP
DSSP (protein)
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein...

 algorithm, the STRIDE assignment criteria also include dihedral angle
Dihedral angle
In geometry, a dihedral or torsion angle is the angle between two planes.The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection...

 potentials. As such, its criteria for defining individual secondary structures are more complex than those of DSSP. The STRIDE energy function
Potential function
The term potential function may refer to:* A mathematical function whose values are a physical potential.* The class of functions known as harmonic functions, which are the topic of study in potential theory.* The potential function of a potential game....

 contains a hydrogen-bond term containing a Lennard-Jones-like
Lennard-Jones potential
The Lennard-Jones potential is a mathematically simple model that approximates the interaction between a pair of neutral atoms or molecules. A form of the potential was first proposed in 1924 by John Lennard-Jones...

 8-6 distance-dependent potential and two angular dependence factors reflecting the planar
Planar
In computer graphics, planar is the method of representing pixel colours with several bitplanes of RAM. Each bit in a bitplane is related to one pixel on the screen...

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
Probability is ordinarily used to describe an attitude of mind towards some proposition of whose truth we arenot certain. The proposition of interest is usually of the form "Will a specific event occur?" The attitude of mind is of the form "How certain are we that the event will occur?" The...

 factors derived from empirical examinations of solved structures with visually assigned secondary structure elements extracted from the 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....

.

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. 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. Both STRIDE and DSSP, among other common secondary structure assignment methods, are believed to underpredict pi helices
Pi helix
A pi helix is a type of secondary structure found in proteins. Although thought to be rare, π-helices are actually found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an α-helix...

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