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Downloads and Upgrades: HELM, Forge 10.3, and MedChem Studio 4.0

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The Pistoia Alliance and Quatrro Research have released an extension to the Hierarchical Editing Language for Macromolecules (HELM) biomolecular representation standard.

HELM provides a mechanism for representing complex biomolecules such as proteins and nucleotides, whose size and complexity make existing small-molecule and sequence-based informatics methodologies impractical or unusable. HELM, which won this year's Bio-IT Industry Best Practice award, uses a hierarchical mutation to represent macromolecules as polymeric structures with support for unnatural components and chemical modifications.

The current release includes updates to HELM specification documentation, the software toolkit which includes all the functionality needed to implement a HELM-based system, and the macromolecule editor.


Cresset has released version 10.3 of Forge, its computational workbench for ligand-based drug design.

Forge 10.3 includes tools to explore structure sensitivity relationships in the Activity Miner tool, improved conformation hunt settings, create detailed pharmacophores from diverse ligands, and adds selectivity cliffs among other updates.


Simulations Plus has released MedChem Studio 4.0, the latest version of its data mining and in silico design software platform.

Features in this release include advanced optical structure recognition which enables the extraction of chemical structures from images in Word documents, PowerPoint slides, webpages, and so on as well as bug fixes and other enhancements.


The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.