What is the range of the qmean4 scores?
They all provide scores in range [0,1] with one being good. QMEAN4 is a linear combination of four statistical potential terms. It is trained to predict global lDDT score in range [0,1]. The value displayed here is transformed into a Z-score to relate it with what one would expect from high resolution X-ray structures.
What are the local scores in qmeanbrane?
The local scores are a linear combinations of the 4 statistical potential terms as well as the agreement terms evaluated on a per residue basis. They are as well in the range [0,1] with one being good. QMEANBrane is a version of QMEAN developed to assess the local quality of alpha-helical transmembrane protein models.
What is the qmeandisco global score and error estimate?
The QMEANDisCo global score is the average per-residue score and the provided error estimate is based on global QMEANDisCo scores estimated for a large set of models and represents the root mean squared difference ( i.e. standard deviation) between QMEANDisCo global score and lDDT (the ground truth).
What is the difference between qmean4 and qmean6?
There are two global score values, QMEAN4 and QMEAN6. QMEAN4 is a linear combination of four statistical potential terms. QMEAN6 additionally uses two agreement terms evaluating the consistency of structural features with sequence based predictions.
What is a good Qmean score?
QMEAN z-scores around zero indicate good agreement between the model structure and experimental structures of similar size. Models of low quality typically have scores of -4.0 or lower. The “thumbs-up” and “thumbs-down” symbols next to the score are used to indicate whether or not the model is of good quality (9).
What is a Qmean 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 GMQE score?
GMQE (Global Model Quality Estimation) is is expressed as a number between 0 and 1, reflecting the expected accuracy of a model built with that alignment and template, normalized by the coverage of the target sequence. Higher numbers indicate higher reliability.
How does SWISS-MODEL work?
How does the Swiss model work? Under a Swiss model-style system, teams play a set number of games rather than facing every other team in the league. In the case of the proposed 36-team Champions League, clubs are set to play 10 matches against opponents determined by a seeding system.
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.
What is homology Modelling in bioinformatics?
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").
How accurate is Swiss-model?
SWISS-MODEL is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications.
How can I become a Swiss-model?
How build a model using the DeepView Project ModeGet the template in the correct quaternary state. First, check the correct biological assembly of your template protein. ... Remove all non-amino acid residues. ... Ensure unique chain IDs. ... Target sequence. ... Adjust target–template alignment in DeepView. ... SWISS-MODEL submission.
How do you reference a Swiss-model?
If you are using models from the SWISS-MODEL Server or Repository, please cite the corresponding articles:SWISS-MODEL Workspace/ GMQE. ... SWISS-MODEL Repository. ... Swiss-PdbViewer/ DeepView project mode. ... ProMod3. ... QMEANDisCo. ... QMEANBrane. ... QMEAN. ... Quaternary Structure Prediction/ QSQE.More items...•
What is the UEFA SWISS-MODEL?
So what is the "Swiss model"? Rather than teams being drawn into eight groups of four, as is the case now, all clubs are placed into one giant table. It is based on the Swiss-system tournament used in chess, whereby each team does not play all of the others.
What is Swiss league format?
A Swiss tournament is similar to a Round-Robin tournament in that no players are eliminated. Every player will play every round, and the player with the highest number of points at the end of the tournament is the winner.
What is Swiss PDB?
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.
Abstract
Model quality estimation is an essential component of protein structure prediction, since ultimately the accuracy of a model determines its usefulness for specific applications. Usually, in the course of protein structure prediction a set of alternative models is produced, from which subsequently the most accurate model has to be selected.
INTRODUCTION
In the course of protein structure prediction usually a set of alternative models is produced from which subsequently the final model has to be selected. For this purpose, scoring functions have been developed which aim at estimating the expected accuracy of models.
THE QMEAN SERVER
The user has the possibility to either submit a single model (in PDB-format), or multiple models (as zip- or tar.gz -archive) and the full-length sequence of the target protein (which is needed for secondary structure and solvent accessibility prediction).
EXAMPLE
The start page of the QMEAN server provides a link to an example results page which allows the user to inspect a typical output of the server. A snapshot of the example results page is given in Figure 1 a.
CONCLUSIONS
Identifying the most accurate model among a set of alternatives is a crucial step in protein structure prediction. Here we present the QMEAN server which makes two methods for model quality estimation publicly available: QMEAN and QMEANclust. The QMEAN server addresses both users of protein structure models as well as method developers.