Connect with us

Software

Modeller- Uses & Applications

Published

on

Modeller- Uses & Applications

Modeller is a standalone tool for homology modeling or comparative modeling of proteins 3D structures [1-4]. In this article, we are discussing its different uses and applications in bioinformatics.

Modeller predicts protein 3D structure by satisfying the spatial restraints. It is capable of performing some additional tasks as well. Some of the main uses and applications of Modeller are mentioned below:

  • Predicts protein 3D structure via homology or comparative modeling.
  • It automatically generates a protein structure containing all non-Hydrogen atoms by the satisfaction of spatial restraints.
  • It helps in the comparison of protein structures by aligning multiple structures together.
  • Modeller models loops in protein structure de novo.
  • It optimizes various models with respect to a flexibly defined objective function.
  • It can also search in sequence databases.
  • Performs clustering.
  • It can be used for different types of protein structure modeling including basic, advanced, iterative, difficult, and modeling with cryo-EM data.

References

  1. B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics 54, John Wiley & Sons, Inc., 5.6.1-5.6.37, 2016.
  2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
  3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
  4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.

Further Reading

Homology Modeling vs ab initio Protein Structure Prediction

ab-initio prediction of protein structure: An introduction

Tutorial: Basic protein structure modeling using MODELLER

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Software

How to calculate binding pocket volume using PyVol plugin in PyMol?

Published

on

How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

Continue Reading

Software

How to generate electron density map using Pymol?

Published

on

How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

(more…)

Continue Reading

Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Published

on

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)

Continue Reading

LATEST ISSUE

ADVERT