20151006_PIKAIROS_KNIME_PIMAPS_POSTER

Molecular Activity Landscape & Similarity Analysis Tool

PiMaps is a suite of KNIME nodes designed for the analysis of large-scale pharmaceutical chemical collections.

The current functionality includes:

  • Clustering of up to millions of compounds from pharmaceutical libraries

  • Visualization and manipulation of compound collections using tree maps

  • Similarity assessment between internal and external compound libraries

  • Calculation of representative diversity sets for entire collections

  • Enrichment and deorphanization of compound series

  • Hierarchical identification of compound series

  • Splitting and merging of chemical collections

  • Density evaluation of compound series

PiMaps nodes are optimized for use with structural fingerprints and physicochemical descriptors available through the KNIME Cheminformatics Extensions.

PiMaps nodes are the following:

PiMaps Builder

Map Builder

PiMaps Builder clusters and visualizes onto a 2D map a set of molecules based on their similarity. Clustering is made by a wise combination of K-Means and Tree-Maps.

MapBuilderClustering_512

Tree-Builder

TreeBuilderNode_256

PiMaps Tree-Builder builds and visualizes a dendrogram based on the Tree-Map structure of a PiMap. The dendrogram can be split and coloured interactively to tag compounds based on sub-trees.

TreeBuilderDendogram_512

Similarity

SimilarityNode_256

PiMaps Similarity achieves extremely fast similarity based on the preliminary clustering of compounds into PiMaps. Similarity can be achieved intra or inter maps containing chemical collections.

Diversity

DiversityNode_256

PiMaps Diversity gathers compounds representing the diversity of an input chemical collection. The collection has been previously clustered on a PiMap and the diverse selection is achieved by gathering in a round-robin way the compounds stored in the cells of the map.

Enrichment

Enrichment_256

PiMaps Enrichment adds compounds to an input chemical collection from a second input source of compounds. The enrichment can be achieved to improve diversity and density.

Join PiMaps

JoinMapsNode_256

Join PiMaps achieves different operations on maps :

  • Full – Joins two maps preserving the content of map cells but generating a new map topology.
  • Partial – Projects the compounds of a first map onto a second map preserving the latter topology.
Split PiMaps

SplitMapsNode_256

Split PiMaps creates two distinct maps from the split of an input map. The splitting preserves the clustering of compounds from the initial PiMap cells.

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