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Related Concept Videos

Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...

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Related Experiment Video

Updated: Jul 17, 2026

Solid Phase Synthesis of a Functionalized Bis-Peptide Using "Safety Catch" Methodology
11:42

Solid Phase Synthesis of a Functionalized Bis-Peptide Using "Safety Catch" Methodology

Published on: May 15, 2012

HELM-BERT: Topology-Aware Representations for Chemically Modified Peptides.

Seungeon Lee1, Takuto Koyama1, Itsuki Maeda1

  • 1Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.

Journal of Chemical Information and Modeling
|July 15, 2026
PubMed
Summary

New HELM notation transformer models advance peptide drug discovery by accurately representing complex molecular structures. This improves predictions for cyclic peptide properties and interactions, outperforming existing methods.

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Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
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Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Related Experiment Videos

Last Updated: Jul 17, 2026

Solid Phase Synthesis of a Functionalized Bis-Peptide Using "Safety Catch" Methodology
11:42

Solid Phase Synthesis of a Functionalized Bis-Peptide Using "Safety Catch" Methodology

Published on: May 15, 2012

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Area of Science:

  • Biomolecular modeling
  • Computational chemistry
  • Drug discovery

Background:

  • Current molecular representations struggle to unify chemical modifications and macrocyclic topology in peptides.
  • Atom-level strings obscure macrocyclic connectivity, while protein sequence models miss noncanonical residues and cross-links.

Purpose of the Study:

  • To develop and evaluate a transformer model pretrained on Hierarchical Editing Language for Macromolecules (HELM) notation for peptide representation.
  • To assess the model's performance in predicting cyclic peptide membrane permeability and peptide-protein interactions.

Main Methods:

  • Pretraining an encoder-only transformer directly on HELM notation, which specifies monomer identity and connectivity.
  • Comparing HELM-BERT performance against SMILES-based encoders on membrane permeability and peptide-protein interaction prediction tasks.

Main Results:

  • HELM-BERT achieved superior performance in cyclic peptide membrane permeability prediction (R² = 0.668), outperforming SMILES-based models.
  • HELM-BERT demonstrated advantages in frozen-representation settings and preserved macrocyclic topology.
  • The model showed competitive performance in peptide-protein interaction prediction across benchmarks.

Conclusions:

  • Pretraining directly on notation that explicitly encodes structural constraints, like HELM, offers a powerful strategy for biomolecular modeling.
  • HELM-BERT provides a unified and effective representation for chemically modified and macrocyclic peptides, advancing therapeutic development.