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
Molecular Simulation in Drug Discovery: A Strategic Guide to Core Methods
Overview of key molecular simulation methods — QM, MD, CGMD, MC, BD, LD, DPD — and their strategic applications in drug discovery pipelines.
Jan 8, 2025
How to Validate AlphaFold Structures
Practical guide to checking AlphaFold-predicted protein models using pLDDT, PAE, geometry validation tools, structural comparisons, and functional tests.
Mar 28, 2024
CoumarinDB
Jan 25, 2024
How to build and validate 3D-QSAR models - Insights from Xu et al., 2020
Comprehensive, metric-driven workflow for robust 3D-QSAR modeling, based on Xu et al., 2020 and enriched with cheminformatics best practices.
Jan 13, 2024
How Long Should Molecular Dynamics Simulations Run? A Practical Guide
Guidelines for choosing appropriate MD simulation lengths in protein–ligand systems, with key convergence metrics like RMSD, RMSF, and interaction fingerprints.
Jan 9, 2023