Research Articles
From In Silico to In Vitro: A Practical Guide to Validating Computational Drug Predictions with Experimental IC50 Data
This article provides a comprehensive guide for researchers and drug development professionals on the critical process of validating computational drug activity predictions with experimental IC50 values.
Validating Computational Models for Cancer Target Identification: From AI Algorithms to Clinical Translation
This article provides a comprehensive overview of the methodologies, applications, and validation frameworks for computational models in cancer target identification.
Overcoming the Ternary Complex Prediction Challenge in PROTAC Design: A Guide to Tools, Validation, and Future Directions
Accurate prediction of PROTAC-mediated ternary complex structures is a pivotal yet formidable challenge in rational degrader design.
Computational Strategies for Undruggable Cancer Targets: From AI Design to Clinical Translation
This article provides a comprehensive overview of cutting-edge computational and AI-driven strategies developed to target traditionally undruggable cancer proteins.
Beyond Static Structures: A 2025 Guide to Mastering Protein Flexibility in Molecular Dynamics Simulations
Protein function is governed by dynamic conformational changes, not static structures, making the accurate handling of flexibility a central challenge in molecular dynamics (MD).
Improving Molecular Docking Accuracy for Flexible Binding Sites: A Guide for Drug Discovery
Accurately predicting ligand binding to flexible sites remains a significant challenge in structure-based drug discovery.
Advances in Molecular Dynamics Simulation Analysis for DNA Intercalators: From Binding Mechanisms to Rational Drug Design
This comprehensive review explores the evolving role of molecular dynamics (MD) simulations in characterizing DNA-intercalator interactions, a critical area for anticancer drug development.
MM/PBSA and MM/GBSA in Drug Discovery: A Comprehensive Guide to Binding Affinity Calculation
Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) are popular end-point methods for estimating ligand-binding affinities, occupying a crucial middle ground between fast but less accurate...
Pharmacophore Modeling for Estrogen Receptor Alpha Inhibitors: From Foundational Concepts to AI-Driven Discovery
This article provides a comprehensive exploration of pharmacophore modeling as a pivotal computational strategy for identifying and optimizing Estrogen Receptor Alpha (ERα) inhibitors, a critical therapeutic target in hormone receptor-positive...
Revolutionizing Cancer Target Discovery: A Practical Guide to AlphaFold2 and AlphaFold3 for Structural Prediction
This article provides a comprehensive overview of the transformative impact of AlphaFold2 and AlphaFold3 on cancer target identification and drug discovery.