DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing,…
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there…
How to calculate number of steps (nsteps) for MD simulation run?
While doing molecular dynamics (MD) simulation, it can be difficult to calculate…
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate…
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . Though…
How to obtain ligand structures in PDB format from PDB ligand IDs?
Previously, we provided a similar script to download ligand SMILES from PDB…
cheML.io: ML-generated molecules database
Due to the advancement of machine learning (ML) methods, we can find…
How to obtain SMILES of ligands using PDB ligand IDs?
Fetching SMILE strings for a given number of SDF files of chemical…
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…
What values are considered as good or bad in computational docking?
After performing computational docking, a question that comes to mind most is…
How to calculate binding pocket volume using PyVol plugin in PyMol?
Previously, we provided a tutorial for PyVol plugin installation. In this article,…
How to generate electron density map using Pymol?
Electron density maps are available for most of the protein structures in…
How to download directories and subdirectories from an HTTPS server?
Previously, we provided a Python script to download data over an FTP…
Converting file formats using Openbabel.
Openbabel offers a wide range of operations. One of which is file…
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)…
How to download files from an FTP server using Python?
In this article, we provide a simple Python script to download files…
How to convert the PDB file to PSF format?
VMD allows converting PDB to PSF format but sometimes it gives multiple…
smitostr.py: Python script to convert SMILES to structures.
As mentioned in some of our previous articles, RDKit provides a wide…