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How do I interpret the field point patterns?

Tuesday, 10 July 2012 00:00
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Cresset

A representative field point pattern is shown below. Larger field points represent stronger points of potential interaction. The field points are coloured as follows:

  • Blue: Negative field points (like to interact with positives/H-bond donors on a protein)
  • Red: Positive field points (like to interact with negatives/H-bond acceptors on a protein)
  • Yellow: van der Waals surface field points (describing possible surface/vdW interactions)
  • Gold/Orange: Hydrophobic field points (describe regions with high polarisability/hydrophobicity)
Interpretation of a field point pattern. The size of the point indicates the potential strength of the interaction
Field points

It can be seen that ionic groups give rise to the strongest electrostatic fields. Hydrogen bonding groups also give strong electrostatic fields. Aromatic groups encode both electrostatic and hydrophobic fields. Aliphatic groups such as the iso-propyl group give rise to hydrophobic and surface points but are essentially electrostatically neutral.


What are field points?

Tuesday, 10 July 2012 00:00
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Cresset

For computational efficiency, Cresset’s field technology condenses the molecular fields down to a set of points around the molecule, termed “field points”. Field points are the local extrema of the electrostatic, van der Waals and hydrophobic potentials of the molecule. They can be thought of as extended pharmacophores, with the advantages that their position is directly calculated from the molecule’s physical properties, and they have size/strength information associated with them (so that e.g. not all H-bond donors are treated the same: some make stronger bonds than others). The generation of field points is described in detail in Cheeseright et al, J. Chem. Inf. Model., 2006, 46, 665-676. The four field types are used in unison to describe all the potential interactions that a ligand in a specified conformation can make to a protein.






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