How to preprocess data for clustering in MATLAB?
Data preprocessing is a foremost and essential step in clustering based on…
How to calculate drug-likeness using RDKit?
RDKit allows performing multiple functions on chemical compounds. One is the quantitative…
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
PyVOL is an excellent plugin of Pymol for pocket visualization of proteins.…
sdftosmi.py: Convert multiple ligands/compounds in SDF format to SMILES.
You can obtain SMILES of multiple compounds or ligands in an SDF…
Video Tutorial: Self-Organizing Maps in MATLAB
Here is a video tutorial for performing self-organizing maps in MATLAB .
tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds
We previously provided a Python script to calculate the Tanimoto similarities of…
How to download FASTA sequences from PDB for multiple structures?
In this article, we are going to download FASTA sequences for multiple…
How to define features/predictors of user dataset for SOM analysis in MATLAB?
Most of the examples that demonstrate the SOM analysis use the default…
tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.
RDKit is a very nice cheminformatics software. It allows us to perform…
How to get input values from SOM sample hits plot in Matlab?
The self-organizing map (SOM) sample hits plot in the Matlab shows the…
How to execute matlab from terminal in Ubuntu (Linux)?
While trying to install Matlab , it generally gives an error stating…
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , there are some issues…
How to install ClusCo on Ubuntu (Linux)?
ClusCo is a bioinformatics software to perform clustering and comparison of protein…
Extracting first and last residue from helix file in DSSP format.
Previously, we have provided a tutorial on using dssp_parser to extract all…
dssp_parser: A new Python package to extract helices from DSSP files.
A new Python package named 'dssp_parser' is developed to parse DSSP files.…
How to calculate center of mass of a protein structure using Python script?
Here is a Python script that helps you calculate the center of…
How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual…
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?
Few errors appear when we try to run the LigAlign plugin in…
How to install multiple Pymol versions on Ubuntu (Linux)?
Sometimes we need to access old versions of Pymol . Running some…