Research Articles
Advances in Explicit Solvent Ensemble Generation: From Machine Learning Potentials to Biomedical Applications
This comprehensive review explores cutting-edge computational strategies for generating conformational ensembles in explicit solvents, a critical capability for understanding biomolecular function and drug binding.
Optimizing Ensemble Selection for Thermodynamic Properties: From Biomolecular Dynamics to Materials Discovery
This article provides a comprehensive guide for researchers and scientists on optimizing ensemble selection for predicting thermodynamic properties.
Statistical Accuracy in Molecular Dynamics: Advancing Conformational Ensemble Prediction for Drug Discovery
Accurately characterizing the conformational ensembles of intrinsically disordered proteins (IDPs) and highly dynamic systems is a central challenge in structural biology and drug development.
Sampling Conformational Space of Disordered Proteins: From Dynamic Ensembles to Druggable Targets
Intrinsically disordered proteins (IDPs), constituting 30-40% of the human proteome, lack stable tertiary structures and exist as dynamic conformational ensembles, presenting unique challenges and opportunities for structural biology and drug...
Force Field Accuracy in Biomolecular Recognition: Advances, Applications, and Future Directions
This article provides a comprehensive overview of the critical role force field accuracy plays in computational studies of biomolecular recognition, a process fundamental to drug discovery and understanding cellular function.
Accurate Temperature and Pressure Control in MD Simulations: A Guide to Reliable Ensemble Generation for Biomolecular Research
This article provides a comprehensive guide for researchers and drug development professionals on achieving accurate temperature and pressure control in Molecular Dynamics (MD) simulations.
Understanding and Mitigating Energy Drift in NVE Ensemble Simulations with the Verlet Algorithm
This article provides a comprehensive guide for researchers and scientists on the phenomenon of energy drift in Microcanonical (NVE) ensemble Molecular Dynamics simulations employing the Verlet algorithm.
Achieving Statistical Convergence in Biomolecular Conformational Ensembles: A Guide for Computational and Structural Researchers
Generating statistically converged conformational ensembles is a critical challenge in computational structural biology, particularly for dynamic systems like intrinsically disordered proteins (IDPs) and multi-domain proteins.
Probabilistic MD Chain Growth (PMD-CG): A Revolutionary Framework for Sampling Conformational Ensembles in Disordered Proteins
Characterizing the conformational ensembles of intrinsically disordered proteins (IDPs) is a paramount challenge in structural biology, with direct implications for understanding cellular function and drug discovery.
REST Enhanced Sampling: A Guide to Accelerated Biomolecular Simulations for Drug Discovery
This article provides a comprehensive overview of Replica Exchange with Solute Tempering (REST), an enhanced sampling method that overcomes sampling limitations in molecular simulations of biomolecules.