What is ProCheck software?
EBI Groups Thornton Software PROCHECK. PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
What is Procheck-NMR?
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR. PROCHECK is available free. Download details are given here.
How do I use ProCheck in live update mode?
In live update mode, the PROCHECK will take a reading every 30 s and update the screen. A pair of arrows rotate in the lower right corner during updates Press ESC to exit the live update mode.
How do I configure the ProCheck controller prior to readings?
Use the following steps to configure the PROCHECK controller prior to readings. Turn on the PROCHECK. Press MENU to navigate to the Configuration tab (Figure 1). Use the UP and DOWN buttons to scroll down to Date. Press ENTER. The system date appears in the center of the screen in a mon day, year format (Figure 2).
What is PROCHECK in bioinformatics?
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
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.
How to interpret verify 3d results?
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.
What does a Ramachandran plot tell you?
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 Errat in bioinformatics?
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.
What is verify 3D?
Determines 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, polar, nonpolar etc) and comparing the results to good structures.
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):
How do you cite MolProbity?
Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21. Davis et al.