What does ProSA do?
ProSA (3) is a tool widely used to check 3D models of protein structures for potential errors. Its range of application includes error recognition in experimentally determined structures (4–6), theoretical models (7–10) and protein engineering (11,12).
What is a good Z-score in ProSA?
-6.07The Z-score of -6.07 predicted by ProSA represents the good quality of the model. The Z-score also measures the divergence of total energy of the structure with respect to an energy distribution derived from random conformations.
What is ProSA protein?
The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise.
What is verify3d?
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.
What is Z-score in bioinformatics?
A Z-score is simply the comparison of an actual alignment score with the scores obtained on a set of random sequences by a Monte-Carlo process. Scores are calculated using the Smith & Waterman [SW81] algorithm.
What is Q mean score?
QMEAN, which stands for Qualitative Model Energy ANalysis, is a composite scoring function describing the major geometrical aspects of protein structures. Five different structural descriptors are used. The local geometry is analyzed by a new kind of torsion angle potential over three consecutive amino acids.
What is a good Z-score proteins?
Summarizing: There is a "Z-score" and an "RMS-Z-score". A Z-score should be 0, and most of the time if it is negative it means worse than average, and positive better than average. An RMS Z-score should be close to 1.0.
What is Z-score in homology Modelling?
The Z-score of a protein is defined as the energy separation between the native fold and the average of an ensemble of misfolds in the units of the standard deviation of the ensemble.
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 read 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.
How do you cite Pdbsum?
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank....PDBsum.ContentAuthorsRoman Laskowski & al. (1997)Primary citationPMID 9433130AccessWebsitewww.ebi.ac.uk/pdbsum/8 more rows
How do you cite MolProbity?
Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography.
Abstract
A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures.
INTRODUCTION
The availability of a structural model of a protein is one of the keys for understanding biological processes at a molecular level. The recent advances in experimental technology have led to the emergence of large-scale structure determination pipelines aimed at the rapid characterization of protein structures.
WEB SERVER USAGE
ProSA-web requires the atomic coordinates of the model to be evaluated. Users can supply coordinates either by uploading a file in PDB format or by entering the four-letter code of a protein structure available from PDB. A chain identifier and an NMR model number may be used to specify a particular model.
CONCLUSION
The protein structure community is, to some extent, aware of the fact that the RCSB protein data base contains erroneous structures. But it is quite difficult to spot these errors. Grossly misfolded structures are sometimes revealed after the results of subsequent independent structure determinations become available.
ACKNOWLEDGEMENTS
The authors are grateful to Christian X. Weichenberger who suggested the use of the ABC transporter structures as an example. This work was supported by FWF Austria, grant number P13710-MOB.