Research Articles
AlphaFold 3 vs. Molecular Docking: A Critical Evaluation for Pose Prediction in Drug Discovery
This article provides a comprehensive evaluation of AlphaFold 3's capabilities for protein-ligand pose prediction against established molecular docking methods.
Orthosteric vs. Allosteric Inhibitors: Mechanisms, Therapeutic Applications, and Future Directions in Drug Discovery
This article provides a comprehensive comparison of orthosteric and allosteric inhibitor mechanisms for researchers and drug development professionals.
Bridging the Gap: A Practical Guide to Validating Computational Binding Site Predictions with Experimental Data
This article provides a comprehensive roadmap for researchers and drug development professionals on validating computational binding site predictions.
X-ray Crystallography vs. Cryo-EM: A Strategic Guide for Complex Structure Analysis
This article provides a comprehensive comparison of X-ray crystallography and cryo-electron microscopy (cryo-EM) for determining the structures of complex biological macromolecules.
Advancing Binding Pose Prediction: Current Methods, Challenges, and Future Directions in Computational Drug Discovery
Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design but remains challenging due to limitations in sampling algorithms, scoring functions, and data biases.
Optimizing Weak Protein-Small Molecule Interactions: Strategies for Challenges, Methods, and Clinical Translation
Weak protein-small molecule interactions (KD > 10⁻⁴ M) are increasingly recognized as crucial regulators of biochemical pathways, allosteric regulation, and signaling cascades, yet they present significant challenges for characterization and...
Strategies for Augmenting Limited Binding Pockets in Protein Interfaces: From AI Prediction to De Novo Design
Targeting protein-protein interactions (PPIs) and designing novel protein functions often requires addressing the challenge of limited binding pockets.
Overcoming Protein-Ligand Crystallization Challenges: A Strategic Guide for Structure-Based Drug Discovery
Obtaining high-quality crystals of protein-ligand complexes is a critical yet often limiting step in structural biology and rational drug design.
Improving Specificity for Protein Interaction Hotspots: Computational and Experimental Strategies for Drug Discovery
This article provides a comprehensive resource for researchers and drug development professionals aiming to improve the specificity of protein-protein interaction (PPI) hotspot prediction.
Beyond the Rule: Strategies for Addressing Lipinski Violations in PPI-Targeted Drug Candidates
This article provides a comprehensive analysis for drug development professionals on navigating Lipinski's Rule of Five violations in Protein-Protein Interaction (PPI) modulator candidates.