Research Articles
Molecular Dynamics for Homology Model Refinement: A Practical Guide for Biomedical Researchers
This article provides a comprehensive guide for researchers and drug development professionals on applying Molecular Dynamics (MD) simulations to refine protein homology models.
A Practical Guide to Setting Up Molecular Dynamics Simulations for Cyclic Peptides
This article provides a comprehensive, step-by-step guide for researchers and drug development professionals to set up and run molecular dynamics (MD) simulations for cyclic peptides.
The Verlet Algorithm in Molecular Dynamics: A Complete Guide for Biomedical Researchers
This article provides a comprehensive exploration of the Verlet algorithm, a cornerstone of Molecular Dynamics (MD) simulations.
Molecular Dynamics in Protein Structure Prediction: From Folding Simulations to Integrative Structural Biology
This article explores the evolving role of molecular dynamics (MD) simulations in the field of protein structure prediction, a domain recently revolutionized by deep learning tools like AlphaFold.
Statistical Ensembles in Molecular Dynamics: A Guide for Biomedical Researchers
This article provides a comprehensive guide to the statistical ensembles used in Molecular Dynamics (MD) simulations, tailored for researchers and professionals in drug development.
A Practical Guide to Preparing Initial Structures for Reliable Molecular Dynamics Simulations
This guide provides a comprehensive framework for researchers and drug development professionals to prepare robust initial structures for Molecular Dynamics (MD) simulations.
How to Calculate Diffusion Coefficient from MD Trajectory: A Step-by-Step Guide for Researchers
This article provides a comprehensive guide for researchers and scientists on calculating diffusion coefficients from molecular dynamics trajectories.
Force Fields in Molecular Dynamics: The Engine of Accurate Biomolecular Simulation and Drug Discovery
This article provides a comprehensive overview of the critical role force fields play in Molecular Dynamics (MD) simulations, with a special focus on applications in drug discovery.
Beyond the Peak: A Comprehensive Guide to What Radial Distribution Function (RDF) Can Analyze in Materials Science and Drug Development
This article provides researchers, scientists, and drug development professionals with a complete guide to the analytical power of the Radial Distribution Function (RDF).
Tracking Atomic Motion: How Molecular Dynamics Simulations Reveal Biomolecular Behavior
This article provides a comprehensive overview of Molecular Dynamics (MD) simulations, a computational technique that tracks atomic motion over time by solving Newton's equations of motion.