UNRES server

UNRES server performs coarse-grained molecular dynamics simulations of protein structures using the physics-based UNRES model to predict protein folding, stability, and interactions without requiring ancillary structural database information.

Key Features:

• Physics-Based Coarse-Grained Model: Uses the UNRES force field derived from physics-based principles for coarse-grained representation of proteins.
• Versatile Simulation Capabilities: Supports local energy minimization, canonical molecular dynamics, replica exchange, and multiplexed replica exchange molecular dynamics simulations.
• Input Flexibility: Accepts protein sequence input and optional restraints derived from secondary-structure predictions or small x-ray scattering data, with selectable simulation types and parameters.
• Comprehensive Protein Handling: Handles oligomeric proteins, proteins containing D-amino-acid residues, and structures with disulfide links.
• Simulation Output: Produces minimized structures, trajectories, final models, and analyses of trajectory ensembles, with all simulation output files available for download.

Scientific Applications:

• Protein-Structure Prediction: Enables physics-based prediction of protein tertiary and quaternary structure at a coarse-grained level.
• Protein Folding Studies: Facilitates investigation of folding pathways and conformational ensembles using enhanced-sampling molecular dynamics techniques.
• Stability and Interaction Analysis: Supports analysis of protein stability, oligomerization, and interactions including disulfide-linked and D-residue-containing proteins.
• Design and Engineering Support: Provides simulation data applicable to protein engineering and structure-guided drug design efforts.

Methodology:

Computations employ the physics-based UNRES force field and support local energy minimization, canonical molecular dynamics, replica exchange and multiplexed replica exchange molecular dynamics; optional restraints from secondary-structure predictions or small x-ray scattering data can be applied, and simulations do not rely on ancillary structural database information.