Dr. Muniba Faiza

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba
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260 Articles

DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing,…

Dr. Muniba Faiza

Protein structure & folding information exploited from remote homologs.

Remote homologs are similar protein structures that share similar functions, but there…

Dr. Muniba Faiza

How to calculate number of steps (nsteps) for MD simulation run?

While doing molecular dynamics (MD) simulation, it can be difficult to calculate…

Dr. Muniba Faiza

Pathonoia- A new tool to detect pathogens in RNA-seq data.

Detecting viruses and bacteria in RNA-seq data with less false positive rate…

Dr. Muniba Faiza

How to create a pie chart using Python?

In this article. we are creating a pie chart of the docking…

Dr. Muniba Faiza

AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool . Though…

Dr. Muniba Faiza

How to make swarm boxplot?

With the new year, we are going to start with a very…

Dr. Muniba Faiza

How to obtain ligand structures in PDB format from PDB ligand IDs?

Previously, we provided a similar script to download ligand SMILES from PDB…

Dr. Muniba Faiza

cheML.io: ML-generated molecules database

Due to the advancement of machine learning (ML) methods, we can find…

Dr. Muniba Faiza

How to obtain SMILES of ligands using PDB ligand IDs?

Fetching SMILE strings for a given number of SDF files of chemical…

Dr. Muniba Faiza

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…

Dr. Muniba Faiza

What values are considered as good or bad in computational docking?

After performing computational docking, a question that comes to mind most is…

Dr. Muniba Faiza

How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin installation. In this article,…

Dr. Muniba Faiza

How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in…

Dr. Muniba Faiza

How to download directories and subdirectories from an HTTPS server?

Previously, we provided a Python script to download data over an FTP…

Dr. Muniba Faiza

Converting file formats using Openbabel.

Openbabel offers a wide range of operations. One of which is file…

Dr. Muniba Faiza

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)…

Dr. Muniba Faiza

How to download files from an FTP server using Python?

In this article, we provide a simple Python script to download files…

Dr. Muniba Faiza

How to convert the PDB file to PSF format?

VMD allows converting PDB to PSF format but sometimes it gives multiple…

Dr. Muniba Faiza

smitostr.py: Python script to convert SMILES to structures.

As mentioned in some of our previous articles, RDKit provides a wide…

Dr. Muniba Faiza