KNIME^® Interfaces

testimonials

• Sehr beeindruckend!, Prof. Michael Berthold, KNIME^®-creator and founder of KNIME GmbH

FTrees in KNIME^®

Similarity searching is a task that needs to be performed routinely and oftentimes in conjunction with tools in a workflow.

FTrees applications can easily be scripted and automated. With the release of the KNIME^® components for FTrees, integration with analysiy tools and workflows is now even simpler.

The FTrees-Interface consists of 3 components. The first main component FTrees Generator appends a Feature Tree descriptor to molecules in the data-stream entering the node — the Feature Tree is added to the molecule as a new property.

The second main component FTrees Similarity compares the molecules in the pipeline to queries in a defined query file, and appends the similarity values to the molecules as new properties. The FTrees Similarity component can also be used to

1. filter molecules according to similarity,
2. generate 2D depictions that visualize the FTrees-mapping using colors and
3. compute 3D alignments based on the FTrees-mapping on the fly.

FlexX in KNIME^®

Performing docking calculations is a routine, yet quite delicate task in every structure-based drug discovery process. Rather than framing it as a black-box approach we have made it particularly target-specific. You can now set up your protein-target for docking guided by an interactive wizard in our new FlexX-GUI. After having satisfied yourself with the performance of the docking you may export all settings including the protein in a target-specific project-file (.fxx) which you can simply reference in this FlexX-in-KNIME^® module.

Fragment Spaces in KNIME^®

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 from the Journal of Combinatorial Chemistry. The KnowledgeSpace and other spaces can be downloaded free of charge here.

The KNIME^®-node for FTrees-FS has one input channel accepting either molecules of Feature Trees as queries for a Fragment Space search. The output channel contains the molecules produced as hits from these searches in the currently loaded space. The space as well as several parameters for the search can be conveniently influenced by the user.

FlexS in KNIME^®

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.

Naomi Converter

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).

auxiliary tools

Our suite of KNIME^® nodes also comprises two license-free auxiliary tools:

• The BioSolveIT Interactive Table extends significantly beyond the standard table viewer. It allows for visualizing FTrees mappings and facilitates interactive sorting and filtering.
• The BioSolveIT Viewer allows for simultaneous browsing through 2 streams of molecules in 3D. Therefore it is perfect for visualizing molecule alignments, but can also used for viewing docking poses.

Both tools, the BioSolveIT Interactive Table and the BioSolveIT Viewer support the KNIME^® HiLite mechanism. Therefore they seamlessly integrate into the KNIME^® workspace.

download

The download mechanism follows the install/update philosophy of KNIME^® which has changed completely with KNIME^® 2.3. Please refer to our tutorials how to install the BioSolveIT KNIME^® components for KNIME^® 2.3 for more details.

Briefly the strategy is the following. You configure KNIME^® to Install New Software from now on also at this URL:

If you work with this website you will see a listing of the BioSolveIT KNIME^® Nodes and Tools. Just select the BioSolveIT Interfaces and the binary packages of the tools you want to use (Note: if in doubt rather select them all). Then click "Next" and follow the instructions.

• Requirements:

  —	from version 1.7.1 on KNIME® version 2.5.2 or later is required
  —	the version 1.7.0 and prior versions have been tested and confirmed to work with KNIME® versions 2.4 and 2.5
  —	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 & Nodes –   KNIME SVG Support
  —	the optinal BioSolveIT FTrees Distance Matrix Feature depends on these packages: –   BioSolveIT Interfaces –   KNIME Distance Matrix

• Supported operating systems: Windows and Linux

PLEASE 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.

Alternatively you may use the following links and install the respective package in KNIME^® from your local drive: