Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events.

ABSTRACT: Molecular dynamics (MD) simulations are powerful tools for studying the movement and interactions of molecules, but they can be computationally expensive, especially for large biomolecules like proteins. This is problematic because accurately simulating the motions of these molecules is key to understanding their functions. Enhanced sampling methods, such as Simulated Tempering (ST), temperature Replica Exchange Molecular Dynamics (REMD), and Replica Exchange with Solute Tempering (REST and REST2), have been developed to overcome this challenge by improving the efficiency of MD simulations. This work presents a new enhanced sampling method called Simulated Solute Tempering 2 (SST2) that builds upon the strengths of ST and REST2. SST2 selectively scales the interactions inside a biomolecule

SUBMITTER: Stratmann D 

PROVIDER: S-EPMC12661556 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature