CADD Consulting Blog


  • Docking billions of molecules

    Docking billions of molecules

    The vast chemical space available for screening is expanding rapidly. Molecular docking is a powerful method to screen molecules in silico. In-house clusters often fail to scale effectively for this task, making cloud-based docking an attractive alternative.[1] Advancements in Large-Scale Docking In 2020, an open-source drug discovery platform elevated the field by enabling large-scale docking…

    Read more…

    by


  • Chameleonicity – or not?

    Chameleonicity – or not?

    Alternative title: Permeability rules for beyond Ro5 molecules In this post I want to highlight two stories with permeability rules for molecules in the beyond Rule of 5 (Ro5) space. The first story comes from Chugai and consists of at least two JACS papers (Tanada, Ohta) published in 2023 about the discovery of a clinical…

    Read more…

    by


  • Antibody evolution with AI

    Antibody evolution with AI

    The code from Brian Hie and Peter Kim’s lab in Stanford described in this 2023 Nature Biotech paper can recommend mutations in proteins. Those mutations have been shown experimentally to be beneficial for antigen binding affinity, thermal stability, poly-specific binding, immunogenicity, and viral neutralization. This is amazing and cool, right? I was curious to test…

    Read more…

    by


  • One million molecules docked

    One million molecules docked

    I did my postdoc in a lab where docking of one million molecules was easy. However, while few select people dock even billions of molecules today (Ref1, Ref2), docking of one million molecules is still a challenge for most people – and a low budget. To address the challenge, I used VirtualFlow screening workflows and…

    Read more…

    by


  • Ultra-fast computer build

    Ultra-fast computer build

    It took me a few days to build a high-performance computing machine. Haven’t done this for 20 years. Now the beast is ready, and I am proud it is running. Main asset: a 64 core Threadripper PRO processor. This computer works like a cluster and allows me to run up to 128 calculations in parallel.…

    Read more…

    by


  • CADD Consulting founded

    CADD Consulting founded

    CADD Consulting GmbH is founded, officially incorporated and listed on the Swiss Central Business Index as of Sept 13, 2022: https://www.zefix.ch/en/search/entity/list/firm/1552565 The official business UID is CHE-210.630.161. To found CADD Consulting GmbH, it took 14 days from the first call of the bank, over signing of founding documents with the notary, to the approval resp.…

    Read more…

    by