Bioinformatics Programming
Some common awk bash commands to modify multi-FASTA files
Some basic operations on multi-FASTA sequence files is a tedious task without using bioinformatics p
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In this article. we are creating a pie chart of the docking score of five different compounds docked
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With the new year, we are going to start with a very simple yet complicated topic (for beginners) in
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Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this arti
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Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial t
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Bioinformatics Programming
How to get secondary structure of multiple PDB files using DSSP in Python?
In this article, we will obtain the secondary structure of multiple PDB files present in a directory
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Bioinformatics Programming
vs_analysis_compound.py: Python script to search for binding affinities based on compound names.
Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obt
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In this article, we provide a simple Python script to download files from an FTP server using Python
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VMD allows converting PDB to PSF format but sometimes it gives multiple errors. Therefore, in this a
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As mentioned in some of our previous articles, RDKit provides a wide range of functions. In this art
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Data preprocessing is a foremost and essential step in clustering based on machine learning methods.
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RDKit [1] allows performing multiple functions on chemical compounds. One is the quantitative estima
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You can obtain SMILES of multiple compounds or ligands in an SDF file in one go. Here, we provide a
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Bioinformatics Programming
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 multiple compounds
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Bioinformatics Programming
tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.
RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operation
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In this article, we are providing a few commands that are used to commit changes to GitHub repositor
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Previously, we have provided a tutorial on using dssp_parser to extract all helices including long a
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The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by usi
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A new Python package named ‘dssp_parser‘ is developed to parse DSSP files. This package
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Bioinformatics Programming
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 mass of a protein using the Pymol [1]
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Bioinformatics Programming
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 screening (VS)
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