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Category: Hints and Tutorials

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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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Hints and Tutorials Jupyter Notebook Macinchem Blog Science Apps

Calculate pKa using Rowan

8 February 20258 February 2025 chris

Rowan is a software platform that makes it possible to run high-level quantum chemical calculations through a web interface. In general, running quantum chemical calculations

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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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Data Analysis Tools Hints and Tutorials Macinchem Blog Science Apps Software Reviews

TabPFN on Apple Silicon

31 January 202531 January 2025 chris

A recent paper published in Nature caught my eye, Accurate predictions on small data with a tabular foundation model by Hollmann et al., Here we present

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Structure-aware generative molecular design: from 2D or 3D?

20 January 202520 January 2025 chris

A very nice review of generative models for molecular design from Morgan Thomas. https://cheminformantics.blogspot.com/2024/12/structure-aware-generative-molecular.html Includes Jupyter notebooks for data and analysis.

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Data Analysis Tools Hints and Tutorials Macinchem Blog Science Apps

Alvascience Tools Now Fully Optimized for Apple Silicon

15 January 202515 January 2025 chris

Whilst Apple’s emulation later Rosetta2 that allows X86_64 applications to run on Apple Silicon this is not ideal especially for computationally intensive tasks. The latest

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Hints and Tutorials Macinchem Blog Science Apps

STOUT V2.0: SMILES to IUPAC name conversion using transformer models

31 December 202431 December 2024 chris

An interesting publication, using the IUPAC rules for naming compounds can be a challenge for for complex systems. This paper describes a transformer-based model https://doi.org/10.1186/s13321-024-00941-x

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Hints and Tutorials Macinchem Blog

Using VMD and Gromacs on M4 Macs

4 December 202413 January 2025 chris

A reader asks about running VMD and installing Gromacs on M4 Macs. I don’t use either application and looking on the VMD website there is

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Hints and Tutorials Macinchem Blog Vortex Scripts

Vortex script to export multiple workspaces to individual sdf files.

19 November 202419 November 2024 chris

Sometimes when I’m comparing multiple datasets I end up with 10-20 different Vortex workspaces, for example if I’m comparing commercial screening collections from different vendors.

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Hints and Tutorials Macinchem Blog Science Apps

Boltz-1:Democratizing Biomolecular Interaction Modeling

18 November 202418 November 2024 chris

The Jameel Clinic have just released Boltz-1, an open-source model designed to accurately model complex biomolecular interactions. Boltz-1 is an open-source model which predicts the

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