Research Articles
Thermostat and Barostat Algorithms for MD Ensembles: A Comprehensive Guide for Biomedical Researchers
This article provides a comprehensive analysis of thermostat and barostat algorithms used in Molecular Dynamics (MD) simulations, crucial for researchers in drug development and computational biology.
Validating Machine Learning Potentials Against Quantum Calculations: A Guide for Biomedical Research
This article provides a comprehensive framework for researchers and drug development professionals to validate Machine Learning Potentials (MLPs) against high-fidelity quantum mechanics calculations.
Enhanced Sampling Methods for Rare Event Tracking in Molecular Dynamics: A Comprehensive Guide for Drug Discovery
This article provides a comprehensive comparison of enhanced sampling methods for tracking rare events in molecular dynamics simulations, a critical challenge in computational drug discovery.
Cross-Validating MD Simulations with Cryo-EM and X-ray Data: A Framework for Robust Structural Biology
This article provides a comprehensive guide for researchers and drug development professionals on integrating Molecular Dynamics (MD) simulations with experimental structural data from cryo-electron microscopy (cryo-EM) and X-ray crystallography.
Bridging the Gap: A Practical Guide to Validating MD-Predicted Protein Folding Pathways
This article provides a comprehensive framework for researchers and drug development professionals seeking to validate molecular dynamics (MD) simulations of protein folding pathways against experimental data.
Ab Initio vs. Classical MD: A Comprehensive Guide for Computational Drug Discovery
This article provides a comparative analysis of Ab Initio Molecular Dynamics (AIMD) and Classical Molecular Dynamics (CMD) for researchers and professionals in drug development.
Explicit vs. Implicit Solvent Models in MD: A Comprehensive Guide for Biomolecular Simulation and Drug Design
Molecular dynamics (MD) simulations are indispensable for understanding biomolecular structure and function, but the choice of solvent model critically impacts the accuracy and feasibility of these studies.
Benchmarking Force Fields for Atomic Motion: A Practical Guide for Biomedical Research
This article provides a comprehensive guide for researchers and drug development professionals on evaluating the accuracy of force fields in simulating atomic motion.
Molecular Dynamics vs. Monte Carlo Simulations: A Comprehensive Guide for Computational Drug Discovery
This article provides a comparative analysis of Molecular Dynamics (MD) and Monte Carlo (MC) simulation methods, tailored for researchers and professionals in drug development.
Bridging Theory and Experiment: A Practical Guide to Validating Molecular Dynamics with NMR Data
This article provides a comprehensive guide for researchers and drug development professionals on integrating Molecular Dynamics (MD) simulations with Nuclear Magnetic Resonance (NMR) spectroscopy to validate and analyze atomic-level protein...