HELM Software for Biopolymers

J Chem Inf Model. 2017 Jun 26;57(6):1233-1239. doi: 10.1021/acs.jcim.6b00442. Epub 2017 May 19.


Hierarchical Editing Language for Macromolecules (HELM version 2.0) is a molecular line notation similar to SMILEs but specifically for communicating and managing biopolymer structures. The HELM project, part of the Pistoia Alliance nonprofit organization, has been tasked to develop and promote HELM as a global exchange format and recently released version 2.0 of the specification. Here we will describe the specifics of the HELM v2.0 notation along with the large ecosystem of software to support HELM-based structure management. We will highlight a recent open-source software and database for HELM monomers and a new, simpler approach to deploying a large complicated molecular management system.

MeSH terms

  • Biopolymers / chemistry*
  • Computational Biology / methods*
  • Databases, Factual
  • Internet
  • Software*


  • Biopolymers