What is a Ramachandran outlier?
Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.
What does the Ramachandran plot tell us?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
What is a good Clashscore?
Summary statistics. Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms. * 100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
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What are Rotamer outliers?
A rotamer outlier is simply a conformation that lies outside the outlier contours of the reference dataset, in this case either the Top500 or the Top8000. For residues that have low-energy sidechain conformations, nothing will change.
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What do the phi and psi angles signify in peptides?
Phi (Φ; C, N, Cα, C) and psi (Ψ; N, Cα, C, N) are on either side of the Cα atom and omega (ω; Cα, C, N, Cα) describes the angle of the peptide bond. This is a result of the partial double bond character of the peptide bond which is caused by resonance effects, i.e. delocalized electrons (N-C=O. <-> N+=C-O-).
What are torsion angles in proteins?
A torsion angle, also known as a dihedral angle, is formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds. The backbone of a protein has three different torsion angles. The omega-angle (ω) – around the peptide bond between C and N.
What is CaBLAM outlier?
As a general rule, CaBLAM outliers usually indicate a problem with the orientations for one or more peptide planes. Look for a way to reorient the peptide either to remove clashes or establish hydrogen bonds.
What is MolProbity used for?
MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids.
What is MolProbity tool?
MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. Results are displayed online as 3D graphics and sortable charts.
Where can I find additional information on Ramachandran plot outlier?
Further information can be found in the Close contacts section of the report, as described below. A residue is considered to be a Ramachandran plot outlier if the combination of its φ and ψ torsion angles is unusual, as assessed by MolProbity ( Chen et al., 2010 ).
What does the Ramachandran plot show?
The Ramachandran plot visualizes energetically allowed and forbidden regions for the dihedral angles. For poor quality homology models, many dihedral angles are found in the forbidden regions of the Ramachandran plot. Such deviations usually indicate problems with the structure.
How is the sidechain outlier score calculated?
The sidechain outlier score is calculated as the percentage of residues with an unusual sidechain conformation with respect to the total number of residues for which the assessment is available.
What is the rsrz outlier score?
RSRZ is calculated only for standard amino acids and nucleotides in protein, DNA and RNA chains. A residue is considered an RSRZ outlier if its RSRZ value is greater than 2. The RSRZ outlier score as shown in the slider graph is calculated as the percentage RSRZ outliers with respect to the total number of residues for which RSRZ was computed.
