knime Archives - Pharmacelera | Pushing the limits of computational chemistry Fri, 15 Dec 2023 10:34:26 +0000 en-US hourly 1 https://wordpress.org/?v=6.9.4 https://pharmacelera.com/wp-content/uploads/2022/04/cropped-Linkedin-avatar-32x32.png knime Archives - Pharmacelera | Pushing the limits of computational chemistry 32 32 New Pharmacelera nodes for KNIME https://pharmacelera.com/blog/upgrades/new-knime-nodes/ Wed, 13 Dec 2023 13:58:39 +0000 https://pharmacelera.com/?p=14377 We are pleased to announce a new update of our Pharmacelera KNIME nodes. Access to our tools is enhanced with the update […]

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Picture of Fernando Martin

Fernando Martin

Pre & Post Sales Manager

We are pleased to announce a new update of our Pharmacelera KNIME nodes. Access to our tools is enhanced with the update of our nodes, making them easier to use for scientists who are familiar with KNIME and for first-time users. Not only have we adapted our tools to the latest versions of KNIME, but we have also provided them with new functionalities compared to previous versions.

New knime nodes
Three nodes are now available: Library Preparation and Virtual Screening (PharmScreen) and exaScreen nodes.

What's new?

Let’s take a look at some of the new features:

  • The nodes have been configured so they can always use the latest version of PharmScreen and exaScreen.
  • The exaScreen node is now available! Our latest technology for huge chemical library screening is now available in KNIME, which mean that you can know mine efficiently billions of compounds, obtaining a list of synthesizable and purchasable compounds that can be further analyzed with your preferred cheminformatics workflow.
exascreen workflow
Workflow for exaScreen execution. A new component has been developed for the experiment configuration.
  • The nodes are now compatible with the Pharmacelera API. This option allows you to run your calculations in your own computer, no matter if it is running Linux, Windows or Mac.
  • Need more computer power? An additional feature that comes with the Pharmacelera API is the possibility to run your calculations on an external computer (workstation or cluster), adding the possibility to access to HPC resources.
  • New design for node configuration. KNIME is changing its interface to Modern UI. And our nodes too. This new interface allows to group the configuration elements, so you can easily identify the different options of the node.
Configuration of the Ligand Preparation node.
  • Compatibility with the latest version of KNIME: The latest version is 5.2, so we have made our nodes compatible with it. However, we understand that many users may be using 4.7, so we will maintain compatibility with this version, although we encourage migration.
  • The nodes are accompanied by new components that facilitate the configuration of the input data, like the exaScreen configuration, helping you to load your files and select where to cut your reference molecule.
knime components for exascreen and pharmscreen
New components to easily configure exaScreen and PharmScreen input information.
  • Third party nodes are evolving constantly, so we have reviewed our previous workflows and updated them, including new ones.
Workflow comparing the results between PharmScreen and RDKit.

Try them now!

Want to try the new Pharmacelera nodes? Write us to contact@pharmacelera.com or fill in the form and ask for your license!

KNIME is an open-source platform built to productionize data science from day 1 by a team with a strong scientific background. Today it has a strong user community of 300,000+ across all industries and in over 60 countries.

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]]> PharmScreen for Knime https://pharmacelera.com/blog/partnerships/pharmscreen-for-knime/ Thu, 23 Apr 2020 07:26:48 +0000 https://new.pharmacelera.com/?p=6571 We are happy to announce that PharmScreen, our virtual screening tool is available for Knime. Knime is a free open-source platform that […]

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]]> We are happy to announce that PharmScreen, our virtual screening tool is available for Knime. Knime is a free open-source platform that uses a modular pipeline concept for data analytics, reporting and integration. Knime links different open-source and third-party nodes and workflows, allowing the connection of different tools and methods for the analysis of different data sources, and using an intuitive graphical user interface.

Based on this modular concept, we have developed PharmScreen for Knime. This version includes a list of nodes to run virtual screening campaigns using our ligand-based approach. The nodes take advantage of our  unique hydrophobic descriptors to mine the unexploited chemical space when screening compound libraries. Additionally, we have implemented a list of workflows that will help you executing PharmScreen for different purposes.

List of available nodes

  • The Ligand Preparation node enables the preparation of molecular libraries to run virtual screening campaigns. For instance, this includes conformer generation, minimization and partial charge, as well as LogP calculation.
  • The Virtual Screening node enables the search of new and promising compounds using a field-based molecular alignment and comparison.
Pharmacelera workflow generated in Knime to run a virtual screening campaign

List of available workflows

  • Pharmacelera_Standard_VS: Use this workflow to run a 3D ligand-based virtual screening campaign with PharmScreen in Knime.
  • Pharmacelera_VS_Multiserver: Execute this workflow if you want to run your virtual screening campaign on a variable number of machines.
  • Pharmacelera_LigandPreparation_Multiserver: Use this workflow to prepare you virtual screening library using a variable number of machines.
  • Pharmacelera_VS_ROCcurve: Run a 3D ligand-based virtual screening benchmark with PharmScreen and generate the corresponding ROC curves .
  • Pharmacelera_VS_ChEMBL_Search: This workflow will search the ligands obtained from PharmScreen’s virtual screening in the ChEMBL database.

How to get PharmScreen for Knime?

You can directly download and install the different nodes and workflows in the Knime Hub. To run the nodes, contact us for the corresponding license.

Are you looking for additional workflows? Let us know and we will be happy to help you!

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