Research Articles
PLIP 2025: A Comprehensive Guide to Analyzing Protein-Ligand Interactions for Drug Discovery
This article provides a complete guide to the Protein-Ligand Interaction Profiler (PLIP), an essential open-source tool for detecting non-covalent interactions in structural biology.
Ligand Pose Prediction: Mastering Molecular Docking from Foundations to AI-Driven Advances
This article provides a comprehensive guide to molecular docking for ligand pose prediction, a critical technique in structure-based drug design.
MM-PBSA and MM-GBSA: A Comprehensive Guide to Binding Free Energy Calculations in Drug Discovery
This article provides a thorough exploration of Molecular Mechanics Poisson-Boltzmann/Generalized Born Surface Area (MM-PBSA and MM-GBSA) methods for estimating binding free energies in structure-based drug design.
Measuring Protein-Small Molecule Affinity by Surface Plasmon Resonance (SPR): A Comprehensive Guide from Principles to Practice
This article provides a comprehensive guide for researchers and drug development professionals on utilizing Surface Plasmon Resonance (SPR) to characterize protein-small molecule interactions.
Bio-Layer Interferometry (BLI): A Comprehensive Guide to Binding Kinetics for Drug Development
This article provides a thorough exploration of Bio-Layer Interferometry (BLI), a powerful, label-free optical biosensing technology for real-time biomolecular interaction analysis.
LABind: A Ligand-Aware Deep Learning Framework for Predicting Protein-Ligand Binding Sites
This article explores LABind, a novel structure-based deep learning method that revolutionizes protein-ligand binding site prediction by explicitly incorporating ligand information.
Virtual Screening for Protein-Ligand Binding Sites: Principles, Methods, and Best Practices in Modern Drug Discovery
This article provides a comprehensive overview of virtual screening (VS) for identifying protein-ligand binding sites, a cornerstone of modern computational drug discovery.
Structure-Based Design of Peptide Mimetics: Bridging AI, Chemistry, and Therapeutics
This article provides a comprehensive overview of the cutting-edge computational and AI-driven methodologies revolutionizing the structure-based design of peptide mimetics.
Fragment-Based Drug Discovery for PPI Modulation: Cracking the 'Undruggable' Code
Protein-protein interactions (PPIs), once considered 'undruggable' due to their flat and extensive interfaces, are now being successfully targeted thanks to fragment-based drug discovery (FBDD).
Solvent Accessibility and Hydrophobic Effects: Decoding the Key Drivers of Protein-Ligand Binding Affinity
This article provides a comprehensive analysis of the critical roles played by solvent accessibility and hydrophobic effects in determining protein-ligand binding affinity.