What values are considered as good or bad in computational docking?
How to sort binding affinities based on a cutoff using vs_analysis.py script?
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
How to generate config file for docking using Autodock Tools?
How to install GROMACS on Apple M1 (MacOS)?
How to take snapshots of structure at specific times in GROMACS?
GROMACS: Uses & Applications
Easy installation of GROMACS on Ubuntu 18.04 & 20.04
How to create an index file in GROMACS for MD simulation?
AlphaFill- New algorithm to fill ligands in AlphaFold models.
How to calculate binding pocket volume using PyVol plugin in PyMol?
How to generate electron density map using Pymol?
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
How to download FASTA sequences from PDB for multiple structures?
How to execute matlab from terminal in Ubuntu (Linux)?
HMMER- Uses & Applications
Easy installation of some alignment software on Ubuntu (Linux) 18.04 & 20.04
FEGS- A New Feature Extraction Model for Protein Sequence Analysis
Installing RDPTools on Ubuntu (Linux)
NGlyAlign- A New Tool to Align Highly Variable Regions in HIV Sequences
MOCCA- A New Suite to Model cis- regulatory Elements for Motif Occurrence Combinatorics
vs_Analysis.py: A Python Script to Analyze Virtual Screening Results of Autodock Vina
How to search motif pattern in FASTA sequences using Perl hash?
How to read fasta sequences from a file using PHP?
How to read fasta sequences as hash using perl?
How to make swarm boxplot?
How to obtain ligand structures in PDB format from PDB ligand IDs?
How to obtain SMILES of ligands using PDB ligand IDs?
How to get secondary structure of multiple PDB files using DSSP in Python?
vs_analysis_compound.py: Python script to search for binding affinities based on compound names.
This Month in Bioinformatics- Research Updates of March 2022
This month in Bioinformatics- Research Updates of November 2021
This Month in Bioinformatics- Research Updates of October 2021
This Month in Bioinformatics- Research Updates of June 2021
This Month in Bioinformatics- Research Updates of May 2021
CNN-DDI: A drug-drug interaction prediction method using convolutional neural networks
DrugShot- A new web-based application to retrieve list of small molecules.
Most widely used tools for drug-drug interaction prediction
How to download small molecules from ZINC database for virtual screening?
Prepare receptor and ligand files for docking using Python scripts
How to find a best fit model using IQ-TREE?
Installing TREE-PUZZLE on Ubuntu
Tutorial: Constructing phylogenetic tree using MEGA7
Update: A multi-epitope in silico vaccine candidate designed for Covid-19
Phylogenetics analysis of SARS-CoV-2 spike glycoproteins
How to install Kpax on Ubuntu (Linux)?
How to run do_dssp command (mkdssp) in Gromacs 2022?
Extracting first and last residue from helix file in DSSP format.
SWISS-MODEL: Uses & Applications
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?
How to make an impactful science presentation?
Basic bioinformatics concepts to learn for beginners
A Beginner’s Guide on How to Write Good Manuscripts
What is MANE project?
BLAST+ 2.12.0- A more efficient version of BLAST is available
Tutorial: Vina Output Analysis Using PyMol
Video Tutorial: Autodock Vina Result Analysis with PyMol
Genome editing of human embryos using CRISPR/Cas9- crossing the ethics of gene editing?
How to perform docking in a specific binding site using AutoDock Vina?
BiR: Impact report – July 2016 & More
CoolBox- An open-source toolkit for genomic data visualization
VISPR- A new tool to visualize CRISPR screening experiments
How to install Cortex on Ubuntu?
How to Compress and Decompress FASTQ, SAM/BAM & VCF Files using genozip?
Installing BCFtools on Ubuntu
As mentioned in some of our previous articles, RDKit provides a wide range of functions. In this article, we are using RDKit [1] to draw a...
