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Structure Prediction

SWISS-MODEL: Uses & Applications

Dr. Muniba Faiza

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swissmodel

SWISS-MODEL [1] is a bioinformatics tool that is widely used for protein structure prediction. In this article, we are going to discuss its uses and applications.

SWISS-MODEL predicts protein three-dimensional structure using homology modeling. Some of its basic and advanced uses are described below:

  • The most common application of SWISS-MODEL is structure prediction.
  • It can also be used for the visualization of target-template alignment.
  • Multiple sequences can be submitted for structure prediction by uploading a single file consisting of protein sequences in FASTA format.
  • Target sequences must be unique. It will not accept any file that contains duplicate sequences.
  • Users can also provide a template for the structure prediction of a target sequence.
  • SWISS-MODEL also offers to provide full control over the projects submitted in its workspace. This is called the ‘DeepView Project’. Using this, users can change the modeling parameters.
  • Users are also allowed to select a template for structure prediction.
  • The best predicted structure is selected on the basis of GMQE and QMEAN scores.
  • SWISS-MODEL has a repository [2] that consists of modeled structures.

References

  1. Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., … & Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research46(W1), W296-W303.
  2. Bienert, S., Waterhouse, A., de Beer, T. A., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL Repository—new features and functionality. Nucleic acids research45(D1), D313-D319.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Structural Bioinformatics

How to predict binding pocket/site using CASTp server?

Dr. Muniba Faiza

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Binding site prediction using CASTp server.

The CASTp server allows you to predict the binding sites in a protein [1]. In this article, we will predict binding sites in a protein using the same.

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Software

Protein structure & folding information exploited from remote homologs.

Dr. Muniba Faiza

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protein structure & folding prediction using remote homologs

Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)

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Software

I-TASSER: Uses & Applications

Dr. Muniba Faiza

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I-TASSER: Uses & Applications

I-TASSER [1] is another most widely used bioinformatics software. It is used for protein three-dimensional structure modeling. In this article, we are going to discuss its uses and applications in bioinformatics. (more…)

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Structural Bioinformatics

Homology Modeling vs ab initio Protein Structure Prediction

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Homology Modeling vs ab initio Protein Structure Prediction

In one of our previous articles, we explained the basic methodology involved in the homology modeling of a protein. In this article, we are going to compare the two methods of protein structure prediction: Homology modeling & ab initio prediction. (more…)

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Homology Modeling

Tutorial: Basic protein structure modeling using MODELLER

Dr. Muniba Faiza

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SALI MODELLER [1] is one of the most widely used command-line bioinformatics software for protein structure prediction based on homology modeling. The installation of MODELLER on Ubuntu has already been explained in an article published previously. This article will explain how to perform basic modeling of a protein sequence having a high percent identity with the template. (more…)

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Homology Modeling

Methodology for Homology Modeling of a Simple Protein

Dr. Muniba Faiza

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homology modeling methodology

Previously, we have explained the initial methods involved in the structure prediction of a protein. In that article, we discussed the three basic methods involved in protein structure prediction: Homology modeling, ab-initio, and threading. In this article, we will explain the methodology involved in performing the homology modeling of a simple protein. (more…)

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Structural Bioinformatics

Homology Modeling of α-Glucosidase Enzyme: 3D Structure Prediction

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The word “Homology modeling”, means comparative modeling or sometimes it is known as Template-Based Modeling (TBM), which refers to develop a three dimensional model of a protein structure by extracting the keen information’s from already experimentally known structure of a homologous protein (the template).  The 3D Protein structural information provides great assistance to study the function of different proteins, ligands interactions, dynamics, and Protein-Protein Interactions (PPI). (more…)

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Algorithms

ab-initio prediction of protein structure: An introduction

Dr. Muniba Faiza

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We have heard a lot about the ab-initio term in Bioinformatics, which could be difficult to understand for newbies in the field of bioinformatics. Today, we will discuss in detail what ab-initio is and what are the applicable methods for it. (more…)

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Software

How to perform protein structure modeling using I-Tasser stand-alone tool?

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I-Tasser stands for the iterative threading assembly refinement is a well-known tool for ab-initio structure modeling of proteins [1]. It uses secondary-structure enhanced profile-profile threading alignment (PPA) [2] and iterative structure assembly simulations using a threading assembly refinement program [3]. I-Tasser is used for ab-initio prediction when the similarity of a protein is quite low (<=30%). Mostly, the I-Tasser server [4] is used for this purpose, which can be easily accessed by registering with a valid institutional mail ID.  In this article, we will learn how to predict a protein structure using the I-Tasser standalone version. (more…)

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Structural Bioinformatics

Structural analysis of FOXL2 gene and its role in kidney failure

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FOXL2 gene codes for a protein belonging to the fork-head- winged helix transcription factor. The FOXL2 gene is present on chromosome 3 and is a single exon gene of 2.7 kb coding for a protein comprising of 376 amino acids [1]. (more…)

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