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Day: 11 March 2023

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  • 2023
  • March
  • 11
Reviews Science Apps Software Reviews

A Review of IMPACTS

11 March 202315 April 2023 chris

I’ve been interacting with Molecular Forecaster https://molecularforecaster.com and they have a number of very cool technologies to provide scientists with desktop tools for drug discovery. One of

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Reviews Science Apps Software Reviews

A review of FAst MEtabolizer 2 (FAME2)

11 March 202325 May 2023 chris

Whilst much computational work is undertaken to support, library design, virtual screening, hit selection and affinity optimisation the reality is that the most challenging issues

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Reviews Science Apps Software Reviews

A review of FAst MEtabolizer (FAME)

11 March 20237 May 2023 chris

Whilst much computational work is undertaken to support, library design, virtual screening, hit selection and affinity optimisation the reality is that the most challenging issues

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Data Analysis Tools Reviews Science Apps Software Reviews

Application Review: DataGraph (formally known is DataPlot)

11 March 20237 May 2023 chris

At the recent WWDC 2006 there was a discussion about the need for a simple 2D plotting tool, David Adalsteinsson the author of the scientific

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Reviews Science Apps Software Reviews

A quick look at CypReact

11 March 202311 May 2023 chris

A recent publication described CypReact: A Software Tool for in Silico Reactant Prediction for Human Cytochrome P450 Enzymes DOI. There are a number of tools that

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Hints and Tutorials Vortex Scripts

Generating IUPAC names for molecules

11 March 202326 October 2023 chris

I was recently asked if I could generate IUPAC names for a series of molecules for a patent filing. There are many chemical drawing packages

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Hints and Tutorials Vortex Scripts

Using JDBC Driver to access Athena from Vortex

11 March 202312 May 2023 chris

This tutorial was created by Jackson Pullman (jackson.pullman@yale.edu) Getting Started Amazon Athena is an interactive query service that makes it easy to analyze data in Amazon

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Hints and Tutorials Vortex Scripts

A collection of Vortex scripts to aid cluster analysis

11 March 202310 April 2023 chris

Exploration and sorting large datasets of molecules often involves the use of clustering techniques to group together molecules with similar properties. It can be used

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Hints and Tutorials Vortex Scripts

A Vortex script to calculate the Blood-Brain Barrier (BBB) SCORE

11 March 20234 January 2024 chris

A recent publication described “The Blood–Brain Barrier (BBB) Score” DOI a scoring function to determine the likelihood of a molecule being brain penetrant. The blood–brain barrier (BBB)

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Hints and Tutorials Vortex Scripts

Vortex script to determine the Amino Acids in a collection of peptides

11 March 202312 November 2024 chris

I’ve recently become interested the comparison of the amino amino-acid composition of peptides, to allow comparison of cyclic versus linear peptides, or brain penetrant verses

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Avatar Chris Swain @macinchem ·
6 Feb

Looking at TabPFN with Polaris datasets https://macinchem.org/2025/02/06/looking-at-tabpfn/ #cheminformatics

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Avatar RSC_CICAG @rsc_cicag ·
3 Feb

Don't forget to register for @RSC_BMCS Conformation Design in #DrugDiscovery conference on 3rd March! … #chemistry #medicinalchemistry #NMR #computationalchemistry #biologists

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Avatar Rowan @rowansci ·
31 Jan

RDKit is the standard software for cheminformatics, but RDKit doesn’t integrate naturally with high-accuracy chemistry simulation tools.

Starting from RDKit, it's non-trivial to simulate pKa, optimize conformers w/ ML, score tautomers, &c. There are many posts like this:

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Avatar Chris Swain @macinchem ·
31 Jan

Tabular Prior-data Fitted Network (TabPFN), a tabular foundation model on Apple Silicon. https://macinchem.org/2025/01/31/tabpfn-on-apple-silicon/

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