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How to compare two pairwise alignments using Modeller-10.1?

Dr. Muniba Faiza

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How to compare two pairwise alignments using Modeller-10.1?

Modeller-10.1 [1, 2] is the latest version of the software. We can perform multiple tasks using this software including homology modeling, comparison of alignments and structures, and so on. In this article, we are going to compare two pairwise alignments using Modeller-10.1.

To run modeller, you need to enter a license key. If you have entered a license key during its installation, then you can proceed further otherwise you will have to define one as shown below. You can easily obtain a license key from here. It is free for academic users.

  • Go to home/user/Downloads/modeller-10.1/modlib/modeller
  • Open file ‘config.py’ in a text editor.
  • Write the license key in the second line next to “license=“.

Files required

For comparing alignments, you need two input PDB files and a Python script, namely, ‘compare_alignments.py’. You can find this script inside your modeller directory. For example, if you have installed it in the Downloads directory, then the path to the script would be:

/home/user/Downloads/modeller-10.1/examples/commands/compare_alignments.py

Remember, here user refers to the username in your system.

Preparing input files

Download PDB files that you want to compare and save them inside /home/user/Downloads/modeller-10.1/examples/atom_files directory. You can also remove extra chains from the file.

Preparing Python script

Open the Python script ‘compare_alignments.py‘ and write the names of the input PDB files that you want to compare as shown below.

# Generate and save sequence-sequence alignment:
aln = Alignment(env)
for code in ('1fas', '2ctx'):
mdl = Model(env, file=code)
aln.append_model(mdl=mdl, align_codes=code, atom_files=code)
aln.align(gap_penalties_1d=(-600, -400))
aln.write(file='toxin-seq.ali')

Change the names of the files in line 3 shown in the above code snippet, i.e., “for code in (‘1fas’, ‘2ctx’):”.

Here, we are using the default files: 1fas & 2ctx.

After changing the names, save this file.

Comparing alignments

Use modpy.sh file to run modeller instead of mod10.1. mod10.1 will keep giving you warnings and errors such as

‘import site’ failed

or

‘Could not find platform independent libraries <prefix>’.

To run modeller using modpy.sh, you need Python 2.3 and 3.9 installed.

Now run the script using the following command.

$ /home/user/Downloads/modeller-10.1/bin/modpy.sh python3 /home/user/Downloads/modeller-10.1/examples/commands/compare_alignments.py

If you are not using Python3 then just write python. It will take a few seconds to finish the job and the output will look like this.

comparing alignments output


References

  1. Webb, B., & Sali, A. (2014). Comparative protein structure modeling using MODELLER. Current protocols in bioinformatics47(1), 5-6.
  2. Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000). Comparative protein structure modeling of genes and genomes. Annual review of biophysics and biomolecular structure29(1), 291-325.

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

Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

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Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

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How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

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How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

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Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

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Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to upgrade cmake on Ubuntu/Linux?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)

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Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

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Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

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[Tutorial] Installing Pyrx on Windows.

Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)

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MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

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How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.

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Software

Installing Autodock4 on MacOS.

Dr. Muniba Faiza

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Installing Autodock4 on MacOS

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

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Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

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How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.

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Software

DS Visualizer: Uses & Applications

Dr. Muniba Faiza

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DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.

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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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RNA-seq analysis

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Dr. Muniba Faiza

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Pathonoia- A new tool to detect pathogens in RNA-seq data.

Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].

(more…)

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Software

AlphaFill- New algorithm to fill ligands in AlphaFold models.

Dr. Muniba Faiza

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AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)

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Software

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

Dr. Muniba Faiza

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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…)

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Software

How to generate electron density map using Pymol?

Dr. Muniba Faiza

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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.

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Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Dr. Muniba Faiza

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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…)

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Software

How to execute matlab from terminal in Ubuntu (Linux)?

Dr. Muniba Faiza

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How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

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Software

How to install Kpax on Ubuntu (Linux)?

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How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

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Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

Dr. Muniba Faiza

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How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)

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Software

Installing SMINA on Ubuntu (Linux).

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Installing SMINA on Ubuntu (Linux)

SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on Ubuntu (Linux). (more…)

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