Skip to content

Macs in Chemistry

A site for chemists using Macs in Chemistry

  • Home
  • Blog
  • Hints and Tutorials
    • Hints and Tutorials
      • Applescript
      • Other Tips
      • Jupyter Notebook
      • Vortex Scripts
  • iBabel
  • Science Apps
  • Reviews
    • Reviews
    • Apple Silicon
    • Software Reviews
      • Reviews
      • Data Analysis Tools
        • Open Source Python Data Science Libraries
      • Spectroscopy
      • Open Source Cheminformatics Toolkits
  • Fortran on a Mac
    • Fortran on a Mac
    • News items

Author: chris

  • Home
  • chris
  • Page 29
Data Analysis Tools Other Tips

Virtual screening/Docking workflow

11 March 20236 May 2023 chris

Whilst high-throughput screening (HTS) has been the starting point for many successful drug discovery programs the cost of screening, the lack of accessibility of a

Read More
Hints and Tutorials Vortex Scripts

Rescoring Docking using RF-Score-VS vortex script

11 March 202318 April 2023 chris

A little while back I described a docking workflow including a rescoring script for Vortex, so I thought it might be useful to include this on a

Read More
Hints and Tutorials Vortex Scripts

Vortex script to make a random selection

11 March 202315 May 2023 chris

Sometimes it is the simplest scripts that prove to be the most useful. I regularly need to select a specified number of molecules in a

Read More
Hints and Tutorials Vortex Scripts

Implementing AB-MPS scoring

11 March 202311 May 2023 chris

Whilst the rule of 5 (Ro5) has provided a useful way to describe small molecule drug space it is also clear that there are a

Read More
Hints and Tutorials Vortex Scripts

Vortex script to flag potential kinase inhibitors

11 March 202315 May 2023 chris

Much of our understanding of the binding of ligands to kinases has come from crystallographic studies, and there are currently several thousand kinase crystal structures

Read More
Hints and Tutorials Other Tips

Downloading from PDB using Python

11 March 202312 April 2023 chris

The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists

Read More
Hints and Tutorials Vortex Scripts

Interacting with Protein Data Bank

11 March 20235 April 2025 chris

The PDB api has been changed so these scripts no longer work, updated scripts can be found here https://macinchem.org/2025/04/05/two-vortex-scripts-for-interacting-with-pdb/ The RCSB Protein Data Bank is an absolutely

Read More
Hints and Tutorials Vortex Scripts

Vortex script to predict sites of metabolism

11 March 20235 May 2023 chris

It is really useful to have two sites of metabolism tools available that use contrasting methodologies, FAME 2 using curated dataset of experimentally determined metabolism

Read More
Hints and Tutorials Vortex Scripts

Vortex script to get PDB information

11 March 202312 April 2023 chris

A while back I published two scripts that use UniChem a web resource provided by the EBI, a ‘Unified Chemical Identifier’ system, designed to assist in the

Read More
Hints and Tutorials Vortex Scripts

A Functional Group Count Vortex Script

11 March 20238 March 2025 chris

I recently wrote a review of Reaction Workflows, a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform

Read More

Posts pagination

Previous 1 … 28 29 30 … 36 Next

Recent Posts

  • Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.
  • OpenADMET Challenge
  • MayaChemTools updated
  • BindFlow
  • ChEMBL 36 is out
Subscribe to the RSS feed

Also now on Bluesky @macinchem.bsky.social

Bluesky feed

  • Get to this post

    @macinchem.bsky.social 21 hours

    Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.

    https://macinchem.org/2025/10/08/use-the-foundation-models-framework-to-access-the-on-device-llm-that-powers-apple-intelligence/
  • Get to this post

    @macinchem.bsky.social 4 days

    OpenADMET Challenge

    https://macinchem.org/2025/10/05/openadmet-challenge/
  • Get to this post

    @macinchem.bsky.social 1 week

    MayaChemTools updated

    https://macinchem.org/2025/10/02/mayachemtools-updated-3/
  • Get to this post

    @macinchem.bsky.social 1 week

    This looks interesting, binding free energy calculations macinchem.org/2025/09/29/b...

    BindFlow – Macs in Chemistry

    macinchem.org

  • Get to this post

    @macinchem.bsky.social 1 week

    BindFlow

    https://macinchem.org/2025/09/29/bindflow/

Archives

  • October 2025
  • September 2025
  • August 2025
  • July 2025
  • June 2025
  • May 2025
  • April 2025
  • March 2025
  • February 2025
  • January 2025
  • December 2024
  • November 2024
  • October 2024
  • September 2024
  • August 2024
  • July 2024
  • June 2024
  • May 2024
  • April 2024
  • March 2024
  • February 2024
  • January 2024
  • December 2023
  • November 2023
  • October 2023
  • September 2023
  • July 2023
  • June 2023
  • May 2023
  • April 2023
  • March 2023
  • February 2023

Categories

  • Applescript
  • Data Analysis Tools
  • Fortran on a Mac
  • Hints and Tutorials
  • iBabel
  • Jupyter Notebook
  • Macinchem Blog
  • meetings
  • Other Tips
  • Reviews
  • Science Apps
  • Software Reviews
  • Spectroscopy
  • Uncategorised
  • Vortex Scripts
  • Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.
  • OpenADMET Challenge
  • MayaChemTools updated
  • BindFlow
  • ChEMBL 36 is out
All Rights Reserved 2024.
Proudly powered by WordPress | Theme: Fairy by Candid Themes.
We use cookies to ensure that we give you the best experience on our website. If you continue to use this site we will assume that you are happy with it.