Tripos Chemistry Extensions for KNIME

Overview

With the rise in popularity and functionality of web-services based architectures, researchers have a choice in how to best access and deploy their favorite informatics products. Tools like KNIME™, the leading open-source data pipelining tool, provide ideal platforms for these researchers by enabling them to cost-effectively string together best-of-breed technologies to process and analyze data-intensive workflows.  The Tripos Chemistry Extensions package introduces chemical intelligence to the highly extensible KNIME platform, providing researchers with the functionality to manipulate, analyze, and visualize chemical data in an open-source workflow environment.

Above: KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows, often referred to as data pipelines, selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.

Tripos Chemistry Extensions for KNIME Brochure (122k)

Tripos Chemistry Extensions package  

The Tripos Chemistry Extensions package complements KNIME’s existing capabilities by providing the Life Sciences industry with access to many important cheminformatics tools, including tools that are used to visualize and transform molecular structures, compute molecular properties, and search for functional groups. 

The Tripos Chemistry Extensions package makes the following cheminformatics functionality (base nodes) accessible from the KNIME framework:

• Property Calculators
• ADME/Tox
• Substructural
• 2D
• Import/ Export to and from the following file types:
• MOL2
• SD
• SLN
• SMILES
• UNITY DB (Import Only)
• SLN Sketcher
• Tanimoto Distance
• JPython Scripting (donated to KNIME, downloadable from www.knime.org)
• UNITY fingerprints
• Structure Validation
• Structure Transformation
• External Tool Node (donated to KNIME, downloadable from www.knime.org)

Separately licensable SYBYL^®-X technologies that are made accessible via the Tripos Chemistry Extensions package include:

• Concord^®
• Confort™
• DBTranslate
• UNITY Similarity (three nodes, a filter, an accumulation and a db search node)
• UNITY 2D (three nodes, a filter, an accumulation and a db search node)
• UNITY 3D query reader
• UNITY 3D search
• UNITY Flex Search
• UNITY Strip Salt
• UNITY Create Database (Linux only)
• HQSAR (two nodes, a model builder and a predictor node)
• SYBYL MSS node (LINUX only)

Additional, separately licensed standalone tools made available via the Tripos Chemistry Extensions package include:

• AUSPYX^®
• Benchware^® 3D Explorer
• Benchware^® DataMiner  

The Tripos Chemistry Extensions for KNIME make use of the following software packages, all of which are bound by the Eclipse Public License 1.0. In accordance with EPL 1.0 section 3.b.iv, the full source code or Eclipse 3.2, GEF 3.2 (w/Draw2D 3.2), and BIRT 2.1 is made available here for download:

Eclipse 3.2 source
Eclipse GEF 3.2 source
Eclipse BIRT 2.1 source