KNIME interfaces

Update: KNIME Support

Unfortunately, KNIME is no longer actively supported by BioSolveIT.
For seasoned users, access to details on legacy workflows for older versions remains available.

However, there's no need to rely on outdated solutions, as BioSolveIT introduces a new workflow environment tailored to the needs of computational chemists and data scientists: HPSee.
HPSee

HPSee

HPSee is a scalable workflow environment designed for high-performance computing. It facilitates the efficient processing of calculations in the context of virtual screening, enabling rapid access to reliable results. By integrating seamlessly with other BioSolveIT platforms, it allows users to achieve their objectives quickly and effectively.

HPSee enables both team coordination and resource-efficient task management with usable interfaces for additional customizability via API.
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Discontinued Workflows

BioSphere

The BioSphere workflow was a tool for constructing and searching vast chemical spaces by integrating user-defined reactions with the KnowledgeSpace™ library of medicinal chemistry reactions. It allowed users to explore up to 45 billion compounds using FTrees-FS, with automatic docking of hits into protein targets and visualization in SeeSAR. Its flexibility enabled custom reaction definitions, rapid searches, and the identification of novel scaffolds and potential hits.

SpaceXplorer

The SpaceXplorer workflow, formerly "REALizer," streamlined virtual hit triage by efficiently retrieving molecules from Chemical Spaces with BioSolveIT KNIME® nodes. It provided tools for analyzing chemical hits, such as FTrees similarity insights, scaffold-hopping comparisons, ligand-based alignments, and docking poses. This workflow enabled users to move seamlessly from molecule retrieval to detailed analysis and visualization, optimizing the virtual screening process.

CovXplorer

The drug discovery workflow CovXplorer was designed for covalent screening campaigns at any target of interest.
With the augmentation of covalent docking in SeeSAR 13.1, covalent warheads are automatically processed. The features cover:
  • Detection and transformation of 36 most commonly used covalent warheads.
  • Selection of a target residue for covalent docking.
  • Flexible handling/rotation of the formed covalent bond.
Visit the SeeSAR page to learn more about covalent docking.
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FragXplorer

The BioSolveIT FragXplorer workflow was a virtual library builder and docking-workflow for drug design and discovery designed to explore binding sites MedChem-style.
Now, it is implemented as the lightning-quick FastGrow tool in our drug discovery dashboard SeeSAR.
FastGrow supports:
  • evolving a fragment binder (fragment-growing)
  • exploring unaddressed space in a binding site
  • designing a small-molecule library tailor-made for the target at hand
Visit the SeeSAR page to learn more about FastGrow.
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MedChemWizard

The MedChemWizard workflow assisted medicinal chemists with idea generation, ligand design and lead optimization using a number of common functional group transformations and medchem rules-of-thumb.
Now it has converged as the MedChemesis tool into SeeSAR.
Features of MedChemesis include:
  • enumerate new ideas based on bioisosteric replacements and common medicinal chemistry transformations
  • decoration of a compound to increase its binding affinity
  • facilitate scaffold hopping
  • morphing into new chemical and intellectual property space
Visit the SeeSAR page to learn more about MedChemesis.
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BioSolveIT tools in KNIME®
SeeSAR is BioSolveIT's next-generation modeling tool for all drug designers. With an intuitive interface, users can quickly and easily load and visualize protein-ligand complexes alongside an estimated binding affinity as calculated by our unique, proprietary HYDE scoring technology. Additional molecular properties are calculated directly within SeeSAR, whilst custom user properties and descriptors can be included via the SDF Inserter node, allowing the user to interactively sort and filter new ideas. In SeeSAR, ligand atoms are individually depicted not only by atom type, but also by their contribution to binding affinity, allowing the user to rapidly identify potential sites of modification to enhance potency.
Our KNIME® node for predicting small molecule binding affinities (Assess Affinity with HYDE in SeeSAR) allows users to easily access our unique, proprietary HYDE scoring technology non-interactively. Using a pre-prepared binding site, input ligands (SDF or mol2 format) are scored — the outputs are an active-site optimized ligand conformation (SDF) and the predicted binding affinity. These results can easily be sorted by predicted affinity as the node outputs both higher and lower numerical limits of the range.
Performing docking calculations is a routine, yet quite delicate task in every structure-based drug discovery process. We automated the entire process and thereby simplified the UI for you tremendously. All you need to do is provide a PDB and a reference ligand to define a binding site and you are ready to go.
Similarity searching is a task that needs to be performed routinely and oftentimes in conjunction with other tools in a workflow. The FTrees Similarity node compares the molecules in the pipeline to separately provided query molecules. Additionally you may:
  • filter molecules according to similarity
  • generate 2D depictions that visualize the FTrees-mapping using colors
  • compute 3D alignments based on the FTrees-mapping on the fly
Feature Trees Fragment Spaces (FTrees-FS) is a unique technology, which enables the user to perform similarity searches in innumerably large compound spaces. The KNIME®-module comprises the search engine. You may use it for example to perform similarity searches in over 12 billion molecules of the so-called KnowledgeSpace™, which based on chemistry protocols to ensure it comprises synthesizable molecules. The KnowledgeSpace™ can be downloaded free of charge here.
This is the package of choice for generating chemical spaces such as the ones to be searched by FTrees-FS. The package consists of three tools:
  • The Reaction Library Synthesizer takes RXN or SMIRKS as input and builds so-called single-library-spaces (cf. below).
  • The Fragment Space Merger takes single-library-spaces (cf. above) and puts them together in a unified fashion which enables searching with FTrees-FS.
  • The Reaction Library Enumerator works similar to the Synthesizer but enumerates the products of your virtual reaction.
Alignments of small molecules can give much insight into structure activity relationships. This very intuitive interface to our FlexS program allows piping in query and a database to screen.
The generation of trustworthy and realistic 3D coordinates for small organic molecules is of great importance in structure-based drug design and cheminformatics. Our Coord3D tool quickly generates high quality 3D coordinates for small molecules based on gold-standard torsion angle data extracted directly from the Cambridge Crystallographic Data Centre's CSD database. Based on 2D inputs (smiles, SD or mol2 format), the tool will convert and output in 3D in the format of your choice.
The Naomi converter contains a super fast compute-engine that reads and writes compounds in a number of standard file formats. It is also capable of calculating basic molecule properties and to use them for filtering. The engine is able to run in parallel on multi-core machines.

Naomi can convert molecules between different representations (SDF, Mol2, and SMILES) and perform substructure-mappings. In addition it is able to generate high quality 2D images in different graphic file formats (SVG, PNG). These can also be used in KNIME® reports as Naomi can be registered as molecule renderer within KNIME®.

The 2D depictor is based on the latest 2D drawing technology from the Center for Bioinformatics in Hamburg (ZBH).
Help
This is a step-by-step introduction that explains for beginners how to use the BioSolveIT software in KNIME® all the way from the download to a virtual screening workflow executed in parallel:
step-by-step introduction (PDF)

NOTE: In principle any update should seamlessly replace previously installed BioSolveIT KNIME® nodes if these where officially released on our website. However, in some cases this mechanism may fail. Thus, we recommend to first uninstall all prior versions of the BioSolveIT KNIME® nodes before installing the new ones. This can be done very easily if you click on “What is already installed” and follow the instructions.

If you need an older version, please contact us via the support page or email.

Requirements:
  • Only the most recent version of the respective software packages is guaranteed to work with the KNIME® modules
  • The following KNIME extensions are required to install the BioSolveIT KNIME® nodes
    • KNIME Base Chemistry Types and Nodes
    • KNIME SVG Support
  • Supported operating systems: Windows and Linux (partly MacOS)

Install and update BioSolveIT KNIME Interfaces conveniently
by adding this URL to Help → Install New Software within KNIME®:

https://www.biosolveit.de/KNIME/download/biosolveit_knime_nodes

If you prefer downloading and installing the nodes manually, please select one of these packages:

jar file zip file

Get your KNIME Interfaces license:

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