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Year: 2023

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  • 2023
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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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Hints and Tutorials Vortex Scripts

Displaying web pages in Vortex

11 March 202315 May 2023 chris

Well things can change quickly at times, in the last tutorial I wrote.. Vortex has a limited capacity to render HTML, it is however a

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Hints and Tutorials Vortex Scripts

Adding images to Vortex

11 March 20232 June 2023 chris

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but

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Hints and Tutorials Vortex Scripts

Implementing a CNS penetration algorithm in Vortex

11 March 202312 April 2023 chris

It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play

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Hints and Tutorials Vortex Scripts

Using Un1Chem from within Vortex

11 March 20236 April 2023 chris

Un1Chem is a new web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical

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Hints and Tutorials Vortex Scripts

Using MOE to dock ligands selected in Vortex

11 March 202329 June 2023 chris

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web

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Hints and Tutorials Vortex Scripts

Vortex script using predictive models on OCHEM

11 March 202312 May 2023 chris

About OCHEM OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from

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    @macinchem.bsky.social 3 days

    nanoFold a Protein Folding Data-Efficiency Competition

    An interesting way to look for better biological foundation models. The core bet is simple: biological data is expensive. Text and image models...

    https://macinchem.org/2026/04/29/nanofold-a-protein-folding-data-efficiency-competition/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    PyChem-Pro

    I've just added PyChem-Pro to the list of cheminformatics toolkits https://macinchem.org/2023/02/17/open-source-cheminformatics-toolkits/ PyChem is a desktop chemistry application and Python library that combines molecular...

    https://macinchem.org/2026/04/27/pychem-pro/
  • View post by on Bluesky

    @macinchem.bsky.social 4 days

    Open Source Cheminformatics Toolkits

    When I wrote the article entitled A few thoughts on scientific software one of the responses I got was that people did not know about the existence of open-source chemistry...

    https://macinchem.org/2023/02/17/open-source-cheminformatics-toolkits/
  • View post by on Bluesky

    @macinchem.bsky.social 7 days

    Sweet J on Mac App Store

    Calculates the 3J coupling constant from the dihedral angle and the electronegativity of the substituents using either the Altona equation or a generalised Karplus equation. Sweet J can be downloaded...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    AI Discovery Awards

    AI Discovery by Nebius is an annual awards for startups that are leveraging AI to revolutionize drug discovery, biotechnology, genomics and HealthTech.. Details are here https://nebius.com/ai-discovery-award...

    https://macinchem.org/2026/04/24/ai-discovery-awards/
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