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Category: Jupyter Notebook

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog

TMAP on Apple Silicon

16 April 202422 April 2024 chris

tmap is a very fast visualisation library for large, high-dimensional data sets. It was published in 2020 DOI and the code is available on GitHub

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Data Analysis Tools Hints and Tutorials Jupyter Notebook Macinchem Blog

A Jupyter Notebook to compare similarity between molecules

11 April 202411 April 2024 chris

I’m sometimes asked for a tool to compare the similarity of a list of molecules with every other molecule in the list. I suspect there

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Data Analysis Tools Jupyter Notebook Macinchem Blog

Project Jupyter wins Technical Advancement to Enable Open Science Award

23 March 202423 March 2024 chris

Project Jupyter is the winner of the White House OSTP “Technical Advancement to Enable Open Science” category. Open science relies on technical advancements and infrastructures

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Some new ways to speed RDKit calls up using multiple threads

11 February 202411 February 2024 chris

Another tutorial from Greg Landrum, focussing on how to take advantage of modern multithreaded CPUs. https://greglandrum.github.io/rdkit-blog/posts/2024-02-11-more-multithreading.html Looking at Generating fingerprints, Molecular standardization, Conformer generation, RMSD

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Downloading ligands from the PDB

24 January 202424 January 2024 chris

A previous post described Getting Ligand ID for multiple PDB files, using the PDBe API (https://www.ebi.ac.uk/pdbe/pdbe-services). The result is a csv file containing the ligand

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Another PDB tools Jupyter Notebook

22 January 202422 January 2024 chris

The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)

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Hints and Tutorials Jupyter Notebook

Getting Ligand ID for multiple PDB files

21 January 202422 January 2024 chris

The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Scikit-Mol โ€“ Easy Embedding of RDKit into Scikit-Learn

20 December 202320 December 2023 chris

Scikit-Mol originated during an RDKit hackathon and has gradually evolved into a tool that I looks extremely useful. Scikit-Mol is related to Scikit-learn and molecules,

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Jupyter Notebook Macinchem Blog

MolSetRep

17 December 202317 December 2023 chris

Cambridge Open Engage is the collaborative platform to upload, share and advance early and open research and a recent post caught my eye. Molecular set

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Hints and Tutorials Jupyter Notebook Macinchem Blog Science Apps

BioSimSpace and sire 2023.4.0 released!

21 October 202321 October 2023 chris

Great to hear about the release of BioSimSpace and sire 2023.4.0. New features in sire include support for running alchemical relative free energy calculations directly

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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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Avatar RSC BMCS @rsc_bmcs ·
29 Apr

๐Ÿงช Final Call: Poster Abstracts Due This Friday! ๐Ÿงช

Don't miss your chance to present at the upcoming AI in Chemistry event! We're inviting submissions for poster abstracts until Friday 2nd May!

๐Ÿ“… Deadline for poster abstracts: Friday 2nd May, 2025
๐Ÿ”— Submit here:โ€ฆ

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Avatar Chris Swain @macinchem ·
24 Apr

Using JDBC with Vortex https://macinchem.org/2025/04/24/using-jdbc-with-vortex/

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Avatar Chris Swain @macinchem ·
18 Apr

The latest update to MayaChemTools https://macinchem.org/2025/04/09/mayachemtools-updated-2/ has been updated!

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