Structural Analysis and Verification Server
- Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall...
- D oes extensive checking of many sterochemical parameters of the residues in the model. [ Reference]
- Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the...
Full Answer
How do I run a validation job on the server?
The server is essentially a scaled-down variant of the new wwPDB OneDep deposition system. This means that the first step is to create a "validation account". You will receive an email about where to go and can then proceed to upload a model and a data file. You can only run one validation job per account at a time.
What is the use of a Structure compatibility server?
Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure. Structural descriptors such as backbone conformation, solvent accessibility and hydrogen bonding are used to characterise the structural environment of each residue position.
How do you evaluate a structure?
A structure is evaluated in a 9-residue sliding window. For each such window, the number of interactions of the 6 possible types (CC,CN,CO,NN,NO,OO) is totaled. These six counts are then converted to fractional values by dividing by the total number of interactions.
What is a validation server?
The wwPDB Validation Service (https://validate.wwpdb.org) is a web server that allows users to upload their structures and (optionally) experimental data and generate a wwPDB validation report. This server performs the same validation as you would observe during the deposition process.
How do you validate a structure?
The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.
What are RSRZ outliers?
RSRZ outliers. fraction of polypeptide and/or polynucleotide residues that do not fit the electron density well when compared with other instances of the same residues in structures at similar resolution. Applicable to crystallographic structures.
What is structured validation?
Structured validation allows for the combination of other kinds of validation, along with more complex processing. Such complex processing may include the testing of conditional constraints for an entire complex data object or set of process operations within a system.
What is Errat server?
ERRAT: An Empirical Atom-Based Method for Validating Protein Structures (1993-2015) Online Server. By the early 1990's it had become clear that it was possible to build and refine atomic structures that had reasonably good crystallographic R-values, but which contained serious structural errors.
What is Rmsd in protein structures?
Root mean square deviation (RMSD) is used for measuring the difference between the backbones of a protein from its initial structural conformation to its final position. The stability of the protein relative to its conformation can be determined by the deviations produced during the course of its simulation.
How is Ramachandran plot generated?
The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the C(i),Ca(i),N(i),C(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et.
What is Rotamer outlier?
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.
Who created Verify3D?
Among the first was an approach by Luthy and Bowie in David Eisenberg’s group (Luthy, Bowie, and Eisenberg (1992) Nature 356, 83-85), named Verify3D, which assessed the degree to which the environment (polarity for example) around each amino acid in a structure was statistically consistent with the amino acid type at that position.
When did it become clear that it was possible to build and refine atomic structures that had reasonably good crystallographic answer
By the early 1990’s it had become clear that it was possible to build and refine atomic structures that had reasonably good crystallographic R-values, but which contained serious structural errors.