What is SWISS-MODEL Expasy?
is a fully automated protein structure homology-modelling server, accessible via the Expasy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make protein modelling accessible to all life science researchers worldwide.
What is SWISS-MODEL used for?
SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today.
What does SWISS-MODEL stand for?
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.
What is Z score in SWISS-MODEL?
In SWISS-MODEL the QMEAN z-score represents an estimate of how comparable the model is to experimentally derived structures of similar size. QMEAN z-scores around zero indicate good agreement between the model structure and experimental structures of similar size.
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...•
How can I download model from SWISS-MODEL?
InstructionsExtract that directory, which will then create a SWISS-MODEL_Repository folder)Create a new SWISSMODEL object, pointing it to that folder.Download models for a specified UniProt accession.
What is GMQE in SWISS-MODEL?
GMQE (Global Model Quality Estimate) is a quality estimate which combines properties from the target-template alignment and the template structure.
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 Swiss PDB?
Description. 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.
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 GMQE value?
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.
Why is homology Modelling important?
Homology modeling obtains the three dimensional structure of a target protein based on the similarity between template and target sequences and this technique proves to be efficient when it comes to studying membrane proteins that are hard to crystallize like GPCR as it provides a higher degree of understanding of ...
How to build a homology model using superoxide dismutase
Here, we provide a step-by-step example on how to build a homology model for the Superoxide Dismutase [Cu-Zn] protein from Drosophila melanogaster (SOD, UniprotKB AC: P61851).
How to model the correct oligomeric state of a protein using ornithine carbamoyltransferase
In this example we show how to infer the quaternary structure of Ornithine Carbamoyltransferase from Thermus thermophilus (OTC, UniProtKB AC P96134). OTC is involved in arginine biosynthesis, where it catalyses the formation of citrulline and phosphate from ornithine and carbamoyl phosphate.
How build a model using the DeepView Project Mode
In order to demonstrate how to use DeepView to build oligomeric assemblies, we are going to build a model of the protease of murine leukemia virus based on the PDB file 3S43. (Please keep in mind that this is just an example to illustrate the workflow; presumably, there would be much better templates available.)
How to build a model for a hetero-oligomeric protein using hemoglobin
In this example, we are going to build a model of the hemoglobin from Physeter macrocephalus (Sperm whale). Hemoglobin is the oxygen-carrying protein of red blood cells. It is made up of four protein chains (globulins) connected together to form a heterotetramer.
Structure Assessment Introduction
The Model Results page of SWISS-MODEL provides the user with an essential, first glance view of a homology model showing ligands, global and local quality, target-template alignments.
Structure Assessment Input
SWISS-MODEL homology models can be sent directly to the Structure Assessment page. Open the drop down menu within the model details on the results page of your SWISS-MODEL project.
Ramachandran Plots
A Ramachandran plot is a way to visualize energetically favoured regions for backbone dihedral angles against of amino acid residues in protein structure. Wikipedia
MolProbity
MolProbity is a structure-validation web service that provides evaluation of model quality at both the global and local levels for both proteins and nucleic acids.
Quality Estimate
QMEAN ( Studer et al. ) is a composite estimator based on different geometrical properties and provides both global (i.e. for the entire structure) and local (i.e. per residue) absolute quality estimates on the basis of one single model. Please read the SWISS-MODEL help and for full details, please refer to the publication .
Residue Quality
The residues found in all protein polypeptide chains of the model are displayed in an interactive sequence display. Each residue is displayed by its one letter code below a bar chart displaying the QMEAN local quality estimation value.