Here is a Python script that helps you calculate the center of mass of a protein using the Pymol [1]. Make sure that you have installed Pymol on your system otherwise, you will get an error stating “No Pymol module found”. If Pymol is not in your path, then…

MANE is a collaborative project between NCBI and EMBL-EBI. It stands for Matched Annotation from NCBI and EMBL-EBI [1]. The datasets provided by NCBI and EMBL-EBI on the human genome are not identical across every gene. The difference between the two datasets…

A new Python package named ‘dssp_parser‘ is developed to parse DSSP files. This package fetches all helices including long and short ones from DSSP files. dssp_parser consists of Python scripts that extract long and short helices in separate files. You have…

The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by using the Biopython package [1]. In this article, we will extract coordinates of C-alpha atoms for each residue from the PDB file using Biopython. Let’s say we…

Previously, we have provided a tutorial on using dssp_parser to extract all helices including long and short separately. Now, we have provided a new python script to find the first and last residue in each helix file. You can extract these residues using…

In this article, we are providing a few commands that are used to commit changes to GitHub repositories using VS code terminal. Committing changes for the first time For committing changes for the first time, follow these steps: Open VS code –> go to Terminal.…

ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In this article, we are going to install ClusCo on Ubuntu (Linux). Installing prerequisites You need to install the TCLAP library in order to run ClusCo. Open…

The self-organizing map (SOM) sample hits plot in the Matlab [1] shows the number of inputs in the neurons but one would be interested in knowing what these input values are. In this article, we are going to get the input values from the neurons. Let’s say…

RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operations on chemical compounds/ ligands. We have provided a Python script to perform fingerprinting using Tanimoto similarity on multiple compounds using RDKit. Introduction…

Most of the examples that demonstrate the SOM analysis use the default Iris dataset. It is also mentioned in the SOM example of MATLAB that for the user dataset, the predictors need to be defined [1]. But it is not quite clear how to define the features or…

In this article, we are going to download FASTA sequences for multiple structures from PDB [1]. We need to have PDB IDs only for input. You can download FASTA sequences as separate files or in a single file for multiple structures in PDB. Follow these steps:…

We previously provided a Python script to calculate the Tanimoto similarities of multiple compounds against each other. In this article, we are providing another Python script to calculate the Tanimoto similarities of one compound with multiple compounds.…

Here is a video tutorial for performing self-organizing maps in MATLAB [1].   References MATLAB. (2022). version 7.10.0 (R2022b). Natick, Massachusetts: The MathWorks Inc.    

Perform SOM clustering and analysis using MATLAB.
Link to SOM code:
https://github.com/MunibaFaiza/som_matlab

Link to website:
https://www.bioinformaticsreview.com

You can obtain SMILES of multiple compounds or ligands in an SDF file in one go. Here, we provide a simple Python script to do that. Let’s say, we have a file in SDF format consisting of molecular structures called ‘ligands.sdf’. In order to perform some…

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. Preparing system Let’s update and upgrade our system first. $ sudo apt-get update $ sudo apt-get upgrade…

RDKit [1] allows performing multiple functions on chemical compounds. One is the quantitative estimation of drug-likeness also known as QED properties. These properties include molecular weight (MW), octanol-water partition coefficient (ALOGP), number of…