How does verify 3D determine the compatibility of an atomic model?
The Verify 3D determine the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop,...
What are the advantages of using 3D profiles for testing models?
An advantage of using 3D profiles for testing models is that profiles have not themselves been used in the determination of the structure. Traditional R-factor tests in X-ray analysis depend on the comparison of observed properties—that is, the X-ray structure factor magnitudes with the same property calculated from the final protein model.
What is a 3D profile of a protein?
This person is not on ResearchGate, or hasn't claimed this research yet. The three-dimensional (3D) profile of a protein structure is a table computed from the atomic coordinates of the structure that can be used to score the compatibility of the 3D structure model with any amino acid sequence.
What are 3D-1D scores?
These numbers are the statistical preferences (called 3D-1D scores) of each of the 20 amino acids for this environment. A profile is computed from the coordinates of a protein model, and it gives a score S for any amino acid sequence folded as the model. To date 3D profiles have found three applications.
What is a good Errat score?
ERRAT is a so-called “overall quality factor” for non-bonded atomic interactions, with higher scores indicating higher quality. The generally accepted range is >50 for a high quality model.
What is errat plot?
ERRAT is a program for verifying protein structures determined by crystallography. Error values are plotted as a function of the position of a sliding 9-residue window.
Why Ramachandran plot is important?
The Ramachandran plot provides a way to view the distribution of torsion angles in a protein structure and shows that the torsion angles corresponding to the two major secondary structure elements (α-helices and β-sheets) are clearly clustered within separate regions.
How do you use Modrefiner?
Cut and paste the structure you want to refine (C-alpha trace, main-chain model or full-atomic model) in PDB format here: Or upload the target structure file from your local computer: Upload a reference structure (only C-alpha trace required) to which the refined model will be driven (Optional):
Verification
At the heart of Verifi3D is a powerful rules-based checking system. As it comes, the service provides a number of standard and popular checking capabilities, but it also has a very intuitive editor to allow users to create their own custom verification sets.
Rules and rulesets
Verifi3D is very much a development tool for creating model validation checks which suit various workflows. This could be anything from one specific rule or rulesets, made up from multiple rules and checked simultaneously.
Conclusion
Currently, there are some seriously big players using the software and assisting in its rapid development – namely Takenaka, BuroHappold Engineering and TBI. Now that the platform has been officially launched, Xinaps can concentrate on adding additional vertical functionality.
Most recent answer
On verify3D, a score of more than 80% means that your model has good quality - however you must check with other evaluation tolls such as voromqa, Proq3 etc to make sure you have a high quality model.
All Answers (9)
You can check Ramachandran Plot from procheck and look for residues in favored regions and outliers. This will give you estimation about your model quality.