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Tag: PDB

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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

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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

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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

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Posts pagination

Previous 1 2

  • View post by on Bluesky

    @macinchem.bsky.social 1 day

    Burette Updated

    Burette is a macOS desktop app and Quick Look extension for molecular previews: Mol* 3D, xyzrender SVG, and RDKit grids. There is a review of Burette here it can...
  • View post by on Bluesky

    @macinchem.bsky.social 2 days

    Avogadro Updated

    Avogadro is an advanced open source molecular editor and visualization tool. Download and installation instructions are here...
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    OpenBind Blind Challenge: Zika virus NS2B-NS3 protease

    On October 14th the OpenBind Blind Challenge was launched, the target is the Zika virus NS2B-NS3 protease. This challenge focuses on predicting how...
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    An Updated Jupyter Notebook for docking

    In 2020 as a result of lockdown I was asked to help create a course for MRes students as an introduction to computer-aided drug design [DOI] that they all...
  • View post by on Bluesky

    @macinchem.bsky.social 2 weeks

    Icms2yield AI-Predicted Full-Spectrum UV Correction Factors: An Analyte-Standard-Free Framework for Reaction Yield Quantification

    https://macinchem.org/2026/10/13/icms2yield-ai-predicted-full-spectrum-uv-correction-factors-an-analyte-standard-free-framework-for-reaction-yield-quantification/

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  • Burette Updated
  • Avogadro Updated
  • OpenBind Blind Challenge: Zika virus NS2B-NS3 protease
  • An Updated Jupyter Notebook for docking
  • Icms2yield AI-Predicted Full-Spectrum UV Correction Factors: An Analyte-Standard-Free Framework for Reaction Yield Quantification
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