Research Articles
Comparative Perturbed-Ensembles Analysis: Decoding Functional Protein Dynamics for Drug Discovery
This article explores Comparative Perturbed-Ensembles Analysis, a powerful computational approach that compares conformational ensembles from molecular dynamics simulations under different perturbations to reveal functional protein dynamics.
Beyond Harmonic Oscillators: Calculating Configurational Entropy in Molecular Dynamics for Drug Discovery
This article provides a comprehensive guide for researchers and drug development professionals on calculating entropic contributions in molecular dynamics (MD) simulations.
Alchemical Transformation Methods: A Comprehensive Guide to Free Energy Calculations in Drug Discovery
This article provides a comprehensive overview of alchemical free energy (AFE) calculations, a powerful set of computational techniques for predicting binding affinities and solvation free energies critical to drug discovery...
NVT Ensemble in Vacuum Simulations: A Practical Guide for Biomedical Research and Drug Development
This article provides a comprehensive guide to the application of the NVT (Canonical) ensemble in vacuum simulations for biomedical and drug discovery research.
Mastering NPT Ensemble for Biomolecular Simulations: A Comprehensive Guide from Theory to Clinical Applications
This article provides a comprehensive guide to the NPT (isothermal-isobaric) ensemble for biomolecular simulations in solution, a fundamental technique for studying biological systems under experimentally relevant conditions.
How to Choose a Statistical Ensemble for MD Simulation: A Guide for Biomedical Researchers
Selecting the appropriate statistical ensemble is a critical, non-trivial step in setting up molecular dynamics (MD) simulations, directly impacting the physical relevance and quantitative accuracy of the results for biomedical...
Configurational Entropy in Intermolecular Interactions: From Theory to Application in Drug Design
This article provides a comprehensive analysis of the critical role configurational entropy plays in governing intermolecular interactions, with a specific focus on biomedical and pharmaceutical applications.
Free Energy and Entropy Calculations: From Theoretical Foundations to Advanced Applications in Drug Discovery
This article provides a comprehensive overview of the theoretical underpinnings and practical computational methods for calculating entropy and free energy, with a special focus on applications in biomolecular interactions and...
Statistical Mechanics for Molecular Dynamics Ensembles: From Theory to Biomedical Applications
This article provides a comprehensive guide to the theory and application of statistical mechanics for generating and validating molecular dynamics ensembles, tailored for researchers and drug development professionals.
Mastering the Constant-Stress NST Ensemble in MD Simulation: A Guide for Biomedical Researchers
This article provides a comprehensive guide to the constant-stress (NST) ensemble in molecular dynamics (MD) simulations, a crucial tool for accurately modeling material and biomolecular responses to anisotropic mechanical stress.