PlayMolecule v2.0 release

Gerard Martínez
Oct 3, 2018 · 3 min read

With the summer heat already waving goodbye and the batteries charged for a new exciting year, we are proud to announce the release of PlayMolecule v2.0! While only few changes are visible from the outside, as the popular saying states: “the beauty lies in the inside”.

What changes?

  • We have undergone a modularity cleanup of all the applications, which are now highly reproducible and portable.
  • We have also released a new landing page, which now gives a clearer overview of the applications offered using a discovery pipeline chart as reference. Do you like the new particles background?
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New landing page
  • In-built benchmarking functionality. We’ve seen that sometimes very simple things can become a real hassle: benchmarking PlayMolecule algorithms can be one. For this reason, in the KDEEP and BindScope applications, if you provide the ground truth (pKd/ΔG for KDEEP and 0/1 for BindScope) we will be able to calculate how good are the algorithms at predicting it. If your input SDF includes a field with the correct type (float for KDEEP, 0/1 integers for BindScope) you will be able to select it as benchmark field, and we will automatically calculate AUC/ROC curve for BindScope and Pearson/Spearman correlation for KDEEP.

What else you’ve got?

  • As you may have noticed, we have also decided to start a new that we will use from now to communicate releases, news, small PlayMolecule tutorials or any information we may feel like sharing with you. We believe that PlayMolecule is nothing without a strong community willing to test and push the boundaries of what’s currently possible and that’s why we want to open this channel of communication with you.
  • We have also created a new Chat Room that you will find on the lower right corner of most of the PlayMolecule pages. This aligns with the previous point: we want to hear from you!
  • We have also made public a new app scoring functionality that aims to evaluate the experience of the users for each of the applications. We have been collecting your opinions for some weeks and we are now starting to share the first results. Thank you for your opinions!
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Each app now displays the average user rating
  • We have also created a new user page that can be accessed through the endpoint. For now, if you are logged in, you will be able to get an overview of the latest jobs you have executed.
  • We have seen that sometimes it is hard to keep track of the test datasets… In order to keep them organized and being able to use files bigger than 50 Mb, we have created a new page called Data Center. In the Data Center you can upload your files (for now only .sdf files), validate them and select them as input from inside the apps (for now available in BindScope and KDEEP). To upload files just drag & drop them in the box below and click on “Upload files”.
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Screenshot of the new section Data Center. Submit files, validate them and get them accessible from the apps.

That’s all for now folks! More content and news coming soon.

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PlayMolecule blog.

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