Molecular PathFinder

Yoshihara Y. and Mori K. (1997). Basic principles and molecular mechanisms of olfactory axon pathfinding. Cell Tissue Res 290, 457-463. 

The molecular interaction fields (MIF) obtainable by GRID [1] may be used to define the solvent accessible surface, which resembles the molecular shape. However, MIFs are descriptors that depend on the 3D-location, and usually several thousand are required to describe a shape. In this chapter we present a novel procedure, called PathFinder, which encodes MIF into a compact alignment-free description of molecular shape. 

The absence of a precise shape description, based on the GRID molecular interaction fields, prompted the development of a new procedure, called PathFinder, that is described here. 

I 5 The Complexity of Molecular Interaction Molecular Shape Fingerprints by the PathFinder Approach... 

Figure 5.3. Schematic view of the Pathfinder procedure the frequency distribution is extracted from GRiD MiF, and is consequentiy encoded into a molecular fingerprint.

We have presented a netv procedure, called PathFinder, aimed at encoding the GRID molecular interaction fields into invariant shape-descriptors, suitable for similarity and complementarity issues. Shape similarity is the underlying foundation of ligand-based methods tvhile shape complementarity is the basis of many receptor-based designs. 

The second section refers to pharmacodynamic aspects and contains chapters on Protein selectivity studies using GRID-MIE by Thomas Fox, The Complexity of Molecular Interaction Molecular Shape Fingerprint by PathFinder Approach by McLay, Hann, Carosati, Cruciani, and Baroni, Alignment-Independent Descip-tors from Molecular Interaction Fields by Manuel Pastor, FLAP 4-point pharma-... 

PathFinder fingerprints are vectorial descriptors encoding information about the molecular shape starting from a surface representation based on molecular interaction fields (MIFs) [McLay, Harm et al, 2006],... 

We would like to thank the M. Hann group (GSK, Stevenage, UK) for granting funds to the research projects in the PathFinder program, our team of coworkers in Perugia and Molecular Discovery (London) for support in implementing the programs. 

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