Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Valence-specific oculomotor abnormalities induced by dynamic video stimuli as a robust biomarker for schizophrenia.

Asian journal of psychiatry·2026

Same author

Impaired Hippocampal Circuitry and Memory Dysfunction in Schizophrenia.

Nature. Mental health·2026

Same author

Near-point-of-care diagnosis of tuberculosis with LyocartE MTB Assay: a multicentre diagnostic accuracy study.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America·2026

Same author

Eye Movement Patterns as Robust Biomarkers for Schizophrenia Identification Using a Novel Data Transformation Approach.

Journal of eye movement research·2026

Same author

IL-21 expression during sublingual immunotherapy for allergic rhinitis.

American journal of clinical and experimental immunology·2026

Same author

Dual-Phase 3D Modified Dixon Steady-State MR Angiography in Pediatric Complex Congenital Heart Disease.

Radiology. Cardiothoracic imaging·2026

Same journal

Correction to "AstraMEV (AI-Guided Structural Assembly of Multi-Epitope Vaccines) Against Infectious Bronchitis Virus".

Journal of chemical information and modeling·2026

Same journal

MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations.

Journal of chemical information and modeling·2026

Same journal

Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.

Journal of chemical information and modeling·2026

Same journal

Structural and Thermodynamic Discrimination between Agonists and Antagonists of Retinoic Acid Receptor γ and the Vitamin D Receptor.

Journal of chemical information and modeling·2026

Same journal

PACEff Builder: An Efficient Platform for Constructing PACE Hybrid-Resolution Models for Molecular Dynamics Simulations of Aqueous Protein, Peptide Assembly, and Membrane Protein Systems.

Journal of chemical information and modeling·2026

Same journal

TransKla: A Local-Global Cross-Attention Based Transformer Approach for Prediction of Lysine Lactylation Sites.

Journal of chemical information and modeling·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 3, 2026

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

Published on: October 2, 2012

HELM Software for Biopolymers.

Jeff Milton¹, Tianhong Zhang², Claire Bellamy³

¹Ionis Pharmaceuticals, Inc , 2855 Gazelle Court, Carlsbad, California 92010, United States.

Journal of Chemical Information and Modeling

|May 5, 2017

Summary

This summary is machine-generated.

The Hierarchical Editing Language for Macromolecules (HELM) v2.0 offers a standardized notation for biopolymer structures. This update includes new software and a simpler system for managing complex molecular data.

More Related Videos

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Published on: January 5, 2017

Related Experiment Videos

Last Updated: Mar 3, 2026

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments

Published on: October 2, 2012

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Online Size-exclusion and Ion-exchange Chromatography on a SAXS Beamline

Published on: January 5, 2017

Area of Science:

Biochemistry
Bioinformatics
Computational Chemistry

Background:

Biopolymer structure representation is crucial for data exchange and management.
Existing notations may lack specificity or comprehensive support for complex biomolecules.
The Pistoia Alliance aims to standardize chemical and biopharmaceutical data formats.

Purpose of the Study:

To introduce the Hierarchical Editing Language for Macromolecules (HELM) version 2.0 specification.
To describe the supporting software ecosystem for HELM-based structure management.
To present novel open-source tools and simplified deployment strategies for HELM.

Main Methods:

Detailed description of the HELM v2.0 notation syntax and features.
Overview of the HELM software ecosystem, including databases and applications.
Demonstration of a new open-source monomer database and deployment approach.

Main Results:

HELM v2.0 provides an enhanced molecular line notation for biopolymers.
A comprehensive software suite supports HELM data management.
New open-source tools simplify the handling of complex macromolecular structures.

Conclusions:

HELM v2.0 advances biopolymer communication and management.
The HELM ecosystem facilitates broader adoption and application of standardized notation.
Simplified tools enhance accessibility for complex molecular data systems.