Understanding Binding Energetics in Molecular Docking
Conceptual overview of the key energetic contributions governing protein–ligand binding in molecular docking, including desolvation, entropy, water displacement, electrostatics, and scoring function behavior.
Mar 13, 2026
Practical System Preparation Tips for Molecular Dynamics Simulations
Preparing a molecular system correctly before running molecular dynamics (MD) simulations is essential for obtaining meaningful and reproducible results. Small technical choices such as solvent box geometry, treatment of protein termini, and strategies for selecting representative conformations can strongly influence simulation stability, computational efficiency, and interpretation of results.
Mar 9, 2026
Stop Using B3LYP/6-31G*: Critical Pitfalls in Modern DFT Calculations and How to Avoid Them
A practical guide to the most common methodological errors in Density Functional Theory calculations, explaining why legacy protocols like B3LYP/6-31G* are no longer reliable and how to adopt robust, modern best practices.
Dec 24, 2025
Ten Critical Pitfalls in Molecular Dynamics Simulations and Strategies for Mitigation
A guide for researchers on avoiding common methodological errors in molecular dynamics, from structure preparation to force field selection and experimental validation.
Dec 21, 2025
How to Use DataWarrior for Drug Discovery: Key Workflows From the Villoutreix Tutorials
Practical introduction to DataWarrior as a free, chemistry-aware workbench for data visualization, filtering, and focused library generation, based on Bruno Villoutreix’s tutorial series.
Nov 15, 2025
Energy Minimization with Open Babel: Practical Guide for Ligand Preparation
Step-by-step workflow for energy minimization of ligands using Open Babel’s obminimize tool, with comparisons of force fields and minimization algorithms for docking and molecular modeling.
Sep 23, 2025
Awesome Drug Discovery
Aug 25, 2025
Principal Component Analysis and Free Energy Landscape Mapping Using GROMACS
Step-by-step workflow for performing PCA and Free Energy Landscape (FEL) analysis from MD simulations with GROMACS.
Jul 9, 2025
Validating Molecular Docking Poses with DFT: A Quick Guide
Learn how to use Density Functional Theory (DFT) to validate docking poses, estimate strain energies, and gain quantum insights into ligand binding.
Jul 3, 2025
Step-by-Step MD Simulation of a Protein–Ligand Complex with GROMACS
A clear workflow for setting up, running, and analyzing a protein–ligand complex simulation using CHARMM36 and TIP3P in GROMACS.
Apr 4, 2025