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Author: chris

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Hints and Tutorials Vortex Scripts

Vortex script Accessing ZINC supplier information

11 March 202315 May 2023 chris

ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 100 million purchasable compounds in ready-to-dock, 3D formats. Sterling and Irwin, J. Chem.

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Hints and Tutorials Vortex Scripts

Vortex Dealing with Greek characters in column names

11 March 20238 June 2023 chris

Just a quick tip. Sometimes I have a column in a Vortex workspace that I want to access via script where the title is something

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Hints and Tutorials Vortex Scripts

Vortex script for flexible search using Un1chem

11 March 202312 April 2023 chris

UniChem is a web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical structures,

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Hints and Tutorials Vortex Scripts

Vortex script for Getting UniChem data from ChEMBL

11 March 202312 April 2023 chris

UniChem is a web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical structures,

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Hints and Tutorials Vortex Scripts

Vortex script to flag potential aggregators

11 March 20235 May 2023 chris

Promiscuous inhibition caused by small molecule aggregation is a major source of false positive results in high-throughput screening. To mitigate this, use of a nonionic

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Hints and Tutorials Vortex Scripts

Importing Open Source Malaria Project data into Vortex

11 March 202311 May 2023 chris

The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date

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Data Analysis Tools Hints and Tutorials Vortex Scripts

Vortex scripting literature searches

11 March 202331 July 2023 chris

Whilst most of the Vortex scripts mentioned on this site to date involve chemical structures we should not forget that Vortex is an excellent general

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Hints and Tutorials Vortex Scripts

Vortex script for Substructure searching very large compound collections.

11 March 202312 April 2023 chris

In an earlier script I described the use of the ability to script multiple sub-structure searches using SMARTS. There are many occasions when this sort

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Hints and Tutorials Vortex Scripts

Vortex script for Accessing ChEMBL web services

11 March 202311 May 2023 chris

ChEMBL is a manually curated chemical database of bioactive molecules . It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory

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Hints and Tutorials Vortex Scripts

Vortex script for Matching muliple SMARTS queries such as PAINS

11 March 202312 April 2023 chris

One of the really neat features of the latest version of Vortex (> build 29622) is the ability to script multiple sub-structure searches using SMARTS.

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Posts pagination

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  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    AlvaSketcher has been updated to include R-group support macinchem.org/2026/09/12/a...
  • View post by on Bluesky

    @macinchem.bsky.social 5 days

    mlxmolkit updated

    mlxmolkit is a GPU-accelerated molecular toolkit using MLX on Apple Silicon, it is a port of nvMolKit that uses Cuda. It now includes AreaWhat it doesEntry pointConformersDrop-in for RDKit EmbedMolecules:...

    https://macinchem.org/2026/09/23/mlxmolkit-updated-2/
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    ChemDoodle Update

    ChemDoodle 2D has been updated. The main focus is expanded support for inorganic compounds and complexes, including haptic bonds and multi-center attachments, their use in formula and mass calculations,...

    https://macinchem.org/2026/09/20/chemdoodle-update/
  • View post by on Bluesky

    @macinchem.bsky.social 2 weeks

    AlvaSketcher

    There a number of chemical drawing packages around that range from lightweight apps for providing structure input to database searches to large fully features packages designed to provide publication...
  • View post by on Bluesky

    @macinchem.bsky.social 3 weeks

    dock-postprocess

    This looks very useful. dock-postprocess is an open-source structure-based drug design toolkit for standardizing docking results and carrying them through restrained OpenMM minimization, pose QC, protein-ligand...

    https://macinchem.org/2026/09/07/dock-postprocess/

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