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swiss model server

by Prof. Fleta Kulas Published 3 years ago Updated 3 years ago

What is SWISS-MODEL server?

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 the 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.

How do you 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 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 Swiss PDB viewer?

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 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.

What is QSQE in SWISS-MODEL?

The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. In general a higher QSQE is "better", while a value above 0.7 can be considered reliable to follow the predicted quaternary structure in the modelling process.

What is Q mean in bioinformatics?

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.

Which web-server is useful in comparative Modelling?

The ModWeb comparative protein structure modeling web-server uses primarily MODELLER for automatic comparative modeling.

How do you use Swiss Prot?

SWISS-PROT provides detailed annotation information on protein sequences. Annotation include information on protein function, post-translational modification of proteins, domains and binding sites, secondary structures, quaternary structures, and diseases associated with protein deficiency.

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.

Pipeline

SWISS-MODEL pipeline comprises the four main steps that are involved in building a homology model of a given protein structure:

Workspace

The SWISS-MODEL Workspace integrates programs and databases required for protein structure modelling in a web-based workspace.

Repository

The SWISS-MODEL Repository provides access to an up-to-date collection of annotated three-dimensional protein models for a set of model organisms of high general interest. Model organisms include human, mouse, C.elegans, E.coli, and various pathogens including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Accuracy and reliability of the method

In the past, the accuracy, stability and reliability of the SWISS-MODEL server pipeline was validated by the EVA-CM benchmark project.

Overview

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. Homology (or comparative) modelling methods make use of experimental protein structures ("templates") to build models for evolutionary related proteins ("targets").

Pipeline

SWISS-MODEL pipeline comprises the four main steps that are involved in building a homology model of a given protein structure:
1. Identification of structural template(s). BLAST and HHblits are used to identify templates. The templates are stored in the SWISS-MODEL Template Library (SMTL), which is derived from PDB.
2. Alignment of target sequence and template structure(s).

Workspace

The SWISS-MODEL Workspace integrates programs and databases required for protein structure modelling in a web-based workspace. Depending on the complexity of the modelling task, different modes of usage can be applied, in which the user has different levels of control over individual modelling steps: automated mode, alignment mode, and project mode. A fully automated mode is used when a sufficiently high sequence identity between target and template (>50%) allows for n…

Repository

The SWISS-MODEL Repository provides access to an up-to-date collection of annotated three-dimensional protein models for a set of model organisms of high general interest. Model organisms include human, mouse, C.elegans, E.coli, and various pathogens including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SWISS-MODEL Repository is integrated with several external resources, such as UniProt, InterPro, STRING, and Nature PSI SBKB.

Accuracy and reliability of the method

In the past, the accuracy, stability and reliability of the SWISS-MODEL server pipeline was validated by the EVA-CM benchmark project. Currently, the SWISS-MODEL server pipeline is participating in the CAMEO3D [1] (Continuous Automated Model EvaluatiOn) project which continuously evaluates the accuracy and reliability of protein structure prediction services in a fully automated manner.

External links

• SWISS-MODEL

See also

• Homology modelling
• Protein structure prediction
• Protein structure prediction software
• CASP (Critical Assessment of Techniques for Protein Structure Prediction)

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