What is a good Qmean value?
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 good Qmean z-score?
Z-scores around 0.0 therefore reflect a "native-like" structure and, as a rule of thumb, a "QMEAN" Z-score below -4.0 indicates a model with low quality. This is illustrated by the "Comparison" plot ((5) in the figure above). The x-axis shows protein length (number of residues).
What is Qmean z-score?
The QMEAN Z-score is an estimate of the "degree of nativeness" of the structural features observed in a model by describing the likelihood that a model is of comparable quality to high-resolution experimental structures.
What is GMQE?
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.
What is Q mean in Swiss model?
QMEAN is a composite scoring function which is able to derive both global (i.e. for the entire structure) and local (i.e. per residue) absolute quality estimates on the basis of one single model. There are two global score values, QMEAN4 and QMEAN6. QMEAN4 is a linear combination of four statistical potential terms.
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 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 Swiss models work?
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.
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 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 a QMean?
QMean is a minimal auto-complete query and ‘did you mean’ suggestion plugin which search for relative keywords and fix typos in words. Its goal is to help users to create relevant queries before sending it to WP search engine.
Does QMean detect similar words?
QMean can detect similar words even if they contain typos! This feature will work on both AJAX suggestions and after the query is searched by showing “Did You Mean: Right Keywords”
Can QMean interact with any word?
QMean can interact by any word user enters individually and complete the query or offer them phrases base on the whole input. Each one has its own advantages so you can set the one suits you.
What does the Q stand for in LGBTQ?
LGBTQ: The first four letters of this standard abbreviation are fairly straightforward: “Lesbian, gay, bisexual and transgender.”. The Q can stand for “questioning” -- as in still exploring one’s sexuality -- or “queer,” or sometimes both.
Is a newborn male or female?
Generally, a newborn’s sex is assigned male or female, though some states and countries provide a third option for those who are intersex.
Is "queer" a slur?
Queer: Once considered a demeaning slur for being gay, “queer” is being reclaimed by some as a self-affirming umbrella term , especially among those who consider other labels restrictive. Some still believe it’s a homophobic slur, so it’s always best to ask or wait for the person whom you’re speaking with to use it.
Introduction to SWISS-MODEL
SWISS-MODEL is a web-based integrated service dedicated to protein structure homology modelling. It guides the user in building protein homology models at different levels of complexity.
The SWISS-MODEL Workspace
The SWISS-MODEL Workspace ( Waterhouse et al.) is a personal web-based working environment, where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals.
Model Building
Models are computed by the SWISS-MODEL server homology modelling pipeline ( Waterhouse et al.) which relies on ProMod3 ( Studer et al. ), an in-house comparative modelling engine based on OpenStructure ( Biasini et al. ).
The SWISS-MODEL Template Library (SMTL)
The SWISS-MODEL template library is a large structural database of experimentally determined protein structures derived from the Protein Data Bank ( Berman et al ).
Input Data
The amino acid sequence of the target protein can be submitted either as plain text, or in FASTA format.
Template search
The degree of difficulty in identifying a suitable template for a target sequence can range from "trivial" for well-characterised protein families to "impossible" for proteins with an unknown fold. The SWISS-MODEL server provides access to a set of increasingly sophisticated methods to search for templates.
Display of modelling results
Coordinates of the model, the corresponding alignment and quality evaluations can be accessed and downloaded via web browser from the workspace.
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.