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Related Experiment Video

Updated: May 25, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Multiscale simulation of small peptides: consistent conformational sampling in atomistic and coarse-grained models.

Olga Bezkorovaynaya1, Alexander Lukyanov, Kurt Kremer

  • 1Max Planck Institute for Polymer Research, Mainz, Germany.

Journal of Computational Chemistry
|February 3, 2012
PubMed
Summary

This study introduces a bottom-up coarse-graining (CG) method for peptides. The CG model accurately reproduces atomistic conformational sampling and allows recovery of microscopic details via backmapping.

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Area of Science:

  • Computational chemistry and biophysics
  • Molecular modeling and simulation

Background:

  • Coarse-graining (CG) simplifies complex molecular systems for efficient simulation.
  • Accurate conformational sampling is crucial for understanding peptide behavior.
  • Bridging CG and atomistic resolutions remains a challenge.

Purpose of the Study:

  • To develop a bottom-up CG procedure for peptides in aqueous solution.
  • To ensure CG models accurately sample conformations matching high-resolution atomistic models.
  • To enable recovery of microscopic details lost during coarse-graining.

Main Methods:

  • Developed a bottom-up coarse-graining procedure for peptides.
  • Determined CG model interactions to match atomistic conformational sampling.

Related Experiment Videos

Last Updated: May 25, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

  • Implemented a backmapping procedure to reintroduce atomistic degrees of freedom (DOF).

    • Main Results:

    • The CG model successfully reproduced correlated degrees of freedom important for secondary structure formation.
    • Microscopic structural details, sometimes lost in CG, were recovered via backmapping.
    • The method links CG descriptions to all-atom models, preserving conformational properties.

    Conclusions:

    • Bottom-up coarse-graining can accurately represent peptide conformational sampling.
    • Backmapping effectively recovers high-resolution structural details from CG models.
    • This approach enables seamless integration of CG and atomistic simulations for biomolecular systems.