Data preprocessing is a foremost and essential step in clustering based on machine learning methods. It removes noise and provides better results. In this article, we...
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...
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...
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.
Here is a video tutorial for performing self-organizing maps in MATLAB [1].
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...
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.
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...
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...
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...
While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
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...
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).
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...
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.
Here is a Python script that helps you calculate the center of mass of a protein using the Pymol [1].
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort...
Running a plugin on an old version of Pymol [1] can give you multiple errors that are not easy to troubleshoot. For example, LigAlign plugin [2]...
Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. For example, if you try to run the ligand_alignment plugin, it...
Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult due to Python incompatibility. New Pymol versions require Python...
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