KNIME® Interfaces

BioSolveIT software available in KNIME® now!

KNIME® the Konstanz Information Miner is a modular, extendable data exploration platform to visually create data pipelines. KNIME® is based on the Java and the Eclipse platform and, through its modular API, easily extensible. When desired, custom nodes and types can be implemented in KNIME® within hours thus extending KNIME® to comprehend and provide first-tier support for highly domain-specific data. This modularity and extensibility permits KNIME® to be employed in commercial production environments as well as teaching and research prototyping settings.

BioSolveIT is a Partner of KNIME® and in the process of making its software-tools accessible to all users via KNIME®. Note that these interfaces are distributed separately of KNIME® and available free of charge. KNIME® itself is distributed under open source license and can be used freely as long as the software or extensions built into it are not distributed for commercial gain (see details on the KNIME® website).

amazing workflows

STORM — small molecule library builder & pocket explorer

BioSolveIT-STORM is a virtual library builder and docking-workflow designed to explore binding sites MedChem-style. It supports:

  • evolving a fragment binder (fragment-growing)
  • exploring un-addressed space in a binding site
  • selecting optimal building blocks for purchase
  • designing a small-molecule library tailor-made for the target at hand

Starting from a template small molecule or fragment in a PDB or proprietary x-ray structure, the user first defines the common element of the library (the unchanging core element), then selects from a pre-installed list the chemical reaction that will create the library (e.g. a particular amide formation). The workflow then docks, scores and ranks all the members of the virtual library, based on the position of the unchanging core. The molecules predicted to be the most potent are then presented for visual inspection in SeeSAR.

download (zip)

The workflow includes example data (where all docking and scoring has been pre-performed). The example shown here is based on a fragment of a known active against Indoleamine 2,3-dioxygenase 1 (IDO1). STORM outputs a number of interesting new ideas for fragment elaboration.

IDO1 is considered as a promising target for the treatment of several diseases, including neurological disorders and cancer. The idea shown on the left uses the Chan-Lam coupling of a Pyrrolidine and might serve as an interesting start point for further optimization.

MedChemWizard — exploring the SAR around a compound hit

testimonials

  • Very impressive!, Prof. Michael Berthold, KNIME®-creator and founder of KNIME GmbH

BioSolveIT tools in KNIME®

SeeSAR
HYDE-scorer
FlexX
FTrees
FTrees-FS
FlexS
3D-generator
Naomi converter
auxiliary tools

tutorial

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)

download

The download mechanism follows the install/update philosophy of KNIME®.

Simply include this URL to Install New Software:

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