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Related Experiment Video

Updated: May 25, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly.

Scott P Carmichael1, M Scott Shell

  • 1Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA.

The Journal of Physical Chemistry. B
|February 4, 2012
PubMed
Summary
This summary is machine-generated.

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A systematic methodology to develop bottom-up coarse-grained models for sequence-specific polypeptoids.

The Journal of chemical physics·2025

This study optimizes coarse-grained peptide models for accurate molecular simulations. The enhanced computational approach efficiently captures peptide folding and fibril assembly, crucial for understanding diseases and biomaterials.

Area of Science:

  • Computational chemistry
  • Biophysics
  • Materials science

Background:

  • Peptide self-assembly is implicated in diseases, pharmaceutical stability, and biomaterial development.
  • Accurate molecular-scale understanding of peptide self-assembly is challenging.
  • Existing coarse-graining methods require optimization for complex systems.

Purpose of the Study:

  • To develop an accurate molecular-scale computational model for peptide self-assembly.
  • To optimize coarse-grained peptide models using a novel multiscale approach.
  • To efficiently simulate complex peptide systems, including folding and fibril formation.

Main Methods:

  • Reformulated coarse-graining methodology based on relative entropy minimization.
  • Employed trajectory-reweighting and perturbation strategies for efficient parameter optimization.

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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

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Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures
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Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures

Published on: June 26, 2020

Related Experiment Videos

Last Updated: May 25, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
09:34

Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

Published on: February 6, 2020

Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures
08:15

Self-Assembly of Gamma-Modified Peptide Nucleic Acids into Complex Nanostructures in Organic Solvent Mixtures

Published on: June 26, 2020

  • Applied the optimized model to a polyalanine case study for folding and fibril assembly.

    • Main Results:

    • Developed an efficient algorithm for optimizing complex coarse-grained peptide models.
    • Created simplified models that accurately reproduce features of detailed all-atom simulations.
    • Demonstrated the model's capability in simulating individual peptide folding and large-scale fibril assembly.

    Conclusions:

    • The multiscale computational approach provides an accurate molecular-level picture of peptide self-assembly.
    • Optimized coarse-grained models offer an efficient way to study complex peptide behaviors.
    • This methodology advances the understanding of peptide self-assembly in disease and biomaterials.