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Tag: rdkit

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Hints and Tutorials Macinchem Blog

Cheminformatics tools that work natively with Google tools such as Sheets and BigQuery

31 March 202531 March 2025 chris

Whilst there are a number of chemistry aware spreadsheets Vortex, Stardrop, Datawarrior, InstantJChem, molsoft etc. many people still use Excel or Google sheets. Vexo is

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog Vortex Scripts

Searching a local copy of PubChem

17 February 202524 February 2025 chris

PubChem is an invaluable source of information about 99 million molecules accessible via a website or programmatically. PubChem is an open chemistry database at the National Institutes

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog Software Reviews

Looking at TabPFN

6 February 202517 February 2025 chris

TabPFN is a foundation model  trained on around 130,000,000 synthetically generated datasets that mimic “real world” tabular data. These datasets sampled dataset size and number

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Jupyter Notebook Macinchem Blog Science Apps

ShEPhERD: Shape, Electrostatics, and Pharmacophore Explicit Representation Diffusion

23 November 202423 November 2024 chris

A really interesting preprint caught my attention from Connor Coley’s group at MIT. ShEPhERD diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design https://arxiv.org/abs/2411.04130v1 …

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Hints and Tutorials Macinchem Blog

Using lwreg with the RDKit cartridge

31 October 202431 October 2024 chris

Fabulous blog post from Greg Landrum, Includes a tutorial on installing PostgreSQL and the cartridge with conda. This post shows how to use the RDKit

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Macinchem Blog

RDKit updated

30 September 202422 October 2024 chris

The 2024.09.1 version of the RDKit was released on the 27th of September and is available via condo-forge (https://anaconda.org/conda-forge/rdkit). Some info on what is new

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Clustering large datasets

13 September 202413 September 2024 chris

Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that

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Hints and Tutorials Macinchem Blog Science Apps

Chemical registration software

12 July 202412 July 2024 chris

The publication describing lwreg is now available. Here, we present lwreg, a lightweight, yet flexible chemical registration system supporting the capture of both two-dimensional molecular

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Macinchem Blog Science Apps

Clipboard-to-SMILES-Converter

28 June 202428 June 2024 chris

I first mentioned this utility back in March and I’ve been using it since then and I have to say I find it invaluable. Clipboard-to-SMILES-Converter

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Macinchem Blog Science Apps

rdEditor

2 May 20242 May 2024 chris

rdEditor is a simple RDKit molecule editor GUI using PySide2. Code is on GitHub https://github.com/EBjerrum/rdeditor?tab=readme-ov-file The paper is on chemrxiv https://chemrxiv.org/engage/chemrxiv/article-details/65e6dcfa9138d23161b2979c

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Avatar RSC BMCS @rsc_bmcs ·
10 Jun

Don't forget to register for the BMCS New approaches to the treatment of Parkinson's meeting ❗

πŸ“… 12th November 2025
πŸ“ Burlington House, London
❗ Abstract submission deadline - 5th September 2025

In the dynamic field of drug discovery, the search for new treatments for…

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Avatar Chris Swain @macinchem ·
9 Jun

Just wanted to highlight New approaches to the treatment of Parkinsons' conference. Awesome lineup of speakers. #BMCSPARKINSONS2025 https://www.cambridgemedchemconsulting.com/news/index_files/493ba583ffb0ec070bb5caf6d7fa9bff-578.html

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Avatar Chris Swain @macinchem ·
8 Jun

WWDC25 is tomorrow https://macinchem.org/2025/06/08/apple-wwdc-2025/

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Avatar Chris Swain @macinchem ·
9 May

We now have a number of confirmed speakers for the New approaches to the treatment of Parkinsons' meeting (Wednesday, 12th November, 2025) , with a couple more just waiting confirmation. Registration is now open https://www.rscbmcs.org/events/parkinsons25/ #BMCSPARKINSONS2025

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