Cheminformatics scientists at a global pharma company site here in Massachusetts have been using a lead-hopping dataset shared by the authors of a scientific article in a prestigious journal several years ago. Using molecular similarity methods to compare their current lead compounds to the dataset, our Client's scientists can generate additional lead compound ideas that have great potential to take their drug lead discovery and optimization projects further.
Keep published methods current with new data
The original paper came out several years ago, and since then there's been a lot of new publicly available data that can and should be added to the dataset. The problem is, the algorithm used to generate the dataset is described in the original paper only succinctly, without all the details. And as any cheminformatician knows, the details matter. Saber Informatics was brought in to reconstruct the published method, to document every step in detail, and to update the dataset with the very latest publicly available data.
QC is key to success in computational methods
We were able to successfully reconstruct every step in the calculations using the authors' published statistics. Working with publicly available assay data can be tricky but were were lucky to have the lead-hopping dataset (kindly made available by the paper's authors) which we used as a benchmark. At every step we performed benchmarking calculations to ensure that correct activity columns of the many available were used, correct assay and compound property filters were applied, etc. In addition to results and code, we delivered detailed documentation of every computational step to our Client to ensure transparency and reproducibility of our results.
Our Client now has an up-to-date lead-hopping dataset that they can themselves update in the future using the code they received as part of the project deliverables. Having documented and run every step as a script, we ensured the quality of our data and therefore the reliability of our Client's lead generation efforts for the immediate future.
Contact us (sales_at_saberinformatics_dot_com) or call us to discuss in confidence the challenges your organization is facing and how we can address them together.
