Ensemble Docking for Binding and Activity Prediction
Limitations of static single-structure docking for flexible targets, and an integrated workflow combining molecular dynamics, clustering, and machine learning.
Jul 5, 2026
Choosing the Right PDB Structure: A Systematic Guide for Docking and MD Simulations
Your docking pose is only as trustworthy as your starting coordinates. Here is a systematic guide to navigating the PDB, avoiding common pitfalls, and future-proofing your workflow for the coming mmCIF era.
May 19, 2026
Computational Strategies for Accelerating Drug Discovery: A Comprehensive Review
A comprehensive walkthrough of cheminformatics, machine learning, molecular docking, ADMET prediction, and molecular dynamics simulations as the modern toolbox for computer-aided drug discovery.
May 10, 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
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
A Quick Guide to Temperature Replica Exchange Molecular Dynamics
Learn how T-REMD enhances conformational sampling in protein–ligand simulations, with setup tips and a GROMACS example workflow.
Aug 3, 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
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
GMXPlotter
Aug 27, 2023