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For this purpose, two different ways of representing the binding site were compared: Sequence based fingerprints and descriptors based on Molecular Interaction Fields (MIFs).
In addition Grid [3] Molecular Interaction Fields (MIFs) can be used to weight and prioritize interacting features.
The more complex 3D descriptors Pentacle (Duran et al., 2008) capture the functional properties of the compounds using molecular interaction fields.
molecular interaction fields.
Hence, we developed novel binding pocket descriptors based on 3D molecular interaction fields.
Molecular Interaction Fields (MIFs) based descriptors can be conveniently used to characterize and compare chromatographic scales.
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The list of genes was analyzed for molecular interactions, Gene Ontology (GO) terms, KEGG pathway annotations, and inferred disease relationships.
Many online repositories, such as Michigan molecular interaction (MiMI; Tarcea et al., 2009), have made extensive gene-wise interaction data readily available.
By contrast, PINK1-deficient mammalian cells show fragmented and truncated mitochondria; nevertheless, the molecular interaction between Parkin and PINK1 is conserved in mammalian cells (Refs 37, 38, 39).
This transformation is very efficient; GSearcher only takes 792 ms to transform a Michigan Molecular Interaction (MiMI; Tarcea et al., 2009) human interaction network of 11 884 nodes and 88 134 edges with 21 attribute fields on a 2.67 GHz Intel Core i7 920 PC.
A comprehensive yeast molecular interaction network containing 23,153 scored protein-protein and protein-DNA interactions was used [ 5] (personal communications, Dr. Anthony Gitter).
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