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).
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What is Prosa used for?
Please cite the following articles if you publish results using ProSA-web: Wiederstein & Sippl (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research 35, W407-W410. Sippl, M.J. (1993) Recognition of Errors in Three-Dimensional Structures of Proteins. Proteins 17, 355-362. This site is …
What is Prosa-web?
21/05/2007 · ProSA is a diagnostic tool that is based on the statistical analysis of all available protein structures. The potentials of mean force compiled from the data base provide a statistical average over the known structures. Structures of soluble globular proteins whose z-scores deviate strongly from the data base average are unusual and frequently such structures turn out to be …
How is the overall quality score calculated by Prosa displayed?
ProSa is a powerful tool in protein structure research. ProSa supports and guides your studies aimed at the determination of a protein's native fold. It is helpful for experimental structure determinations and modeling studies. Suppose you are confronted with the three-dimensional structure of a protein. The structure may have been determined ...
What articles should I cite when I publish results using Prosa-web?
proSA Tools CHRISTOPH MIETHKE GMBH & CO. KG 0297 USA Instructions for Use . 3 proSA Tools | USA CONTENT Remark 4 Indication 5 proSA VERIFICATION TOOL 5 proSA MASTERDISC 5 proSA VERIFICATION COMPASS 6 proSA ADJUSTMENT TOOL 6 proSA ADJUSTMENT DISC 7 Technical description 8 Physics background 9 Function of the proSA 10 Selecting the …
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.
What is protein validation?
WHAT IF also provides an environment for: homology modeling of protein tertiary structures and quaternary structures; validating protein structures, notably those deposited in the PDB; correcting protein structures; visualising macromolecules and their interaction partners (for example, lipids, drugs, ions, and water), ...
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.