PREDITOR (PREDIction of TORsion angles) is a freely available web-server for the prediction of protein
torsion 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 ...
s from
chemical shifts.
For many years it has been known that protein
chemical shifts are sensitive to protein secondary structure, which in turn, is sensitive to backbone
torsion 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 ...
s.
torsion 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 ...
s are internal coordinates that can be used to describe the conformation of a polypeptide chain. They can also be used as constraints to help determine or refine protein structures via
NMR spectroscopy. In proteins there are four major
torsion 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 ...
s of interest: phi, psi, omega and chi-1. Traditionally protein
NMR spectroscopists have used vicinal J-coupling information and the Karplus relation to determine approximate backbone
torsion 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 ...
constraints for phi and chi-1 angles.
However, several studies in the early 1990s pointed out the strong relationship between 1H and 13C chemical shifts and
torsion 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 ...
s, especially with backbone phi and psi angles.
Later a number of other papers pointed out additional chemical shift relationships with chi-1 and even omega angles.
PREDITOR was designed to exploit these experimental observations and to help
NMR spectroscopists easily predict protein
torsion 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 ...
s from
chemical shift assignments. Specifically, PREDITOR accepts protein sequence and/or chemical shift data as input and generates
torsion 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 ...
predictions for phi, psi, omega and chi-1 angles. The algorithm that PREDITOR uses combines
sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Alig ...
,
chemical shift alignment and a number of related
chemical shift analysis techniques to predict
torsion 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 ...
s. PREDITOR is unusually fast (<40 s per protein) and exhibits a very high level of accuracy. In a series of tests 88% of PREDITOR’s phi/psi predictions were within 30 degrees of the correct values, 84% of chi-1 predictions (3-state predictions) were correct and 99.97% of PREDITOR’s predicted omega angles were correct. PREDITOR also estimates the
torsion 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 ...
errors so that its
torsion 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 ...
constraints can be used with standard protein structure refinement software, such as CYANA, CNS, XPLOR and AMBER. PREDITOR also supports automated
protein chemical shift re-referencing and the prediction of proline cis/trans states. PREDITOR is not the only
torsion 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 ...
prediction software available. Several other computer programs including TALOS,
TALOS+
and DANGLE
have also been developed to predict backbone
torsion 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 ...
s from protein
chemical shifts. These stand-alone programs exhibit similar prediction performance to PREDITOR but are substantially slower.
See also
*
Chemical shift
*
Protein Chemical Shift Re-Referencing
*
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 ...
*
Chemical shift index
*
Protein NMR
References
{{Reflist
Protein databases