View HINT Parameters for HASL Dialog Box

HINT Parameters for HASL Dialog Box

Partition Method: option menu: {Calculate|Dictionary}; HINT offers two methods of partitioning the molecule on this option menu: "Calculate" or "Dictionary". The Calculate method uses the molecule's atom types (Sybyl) and bond connections as input data to the partition algorithm. The Dictionary method relies on a predefined set of predefined data for regularly occurring substructures such as amino acid residues and nucleic acid bases. In this case the input data is the atom names and substructure names/types.
Include SASA Factor in Parameter: check box; If this box is checked "on" then the reported HINT parameter passed to HASL will be the product of a_i and S_i where a_i is the hydrophobic atom constant and S_i is the solvent accessible surface area for atom i. If the box is checked "off" only a_i will be passed to HASL. NOTE: be careful in your choice of H-Val Gain Factor in the Main HASL dialog with these two options. The magnitude of the passed HINT parameter is significantly different when calculated these two ways.
Solvent Condition: option menu: {Inferred|Neutral|Acid|Base}; This option menu is active only if the "Dictionary" method is chosen. The menu lists four options: "Inferred", "Neutral", "Base", "Acid". The latter three represent the pH conditions under which the molecule is to be partitioned. Inferred represents a special case where each substructure (e.g., residue) will be partitioned based on its hydrogen count. For example, if one aspartic acid in a protein is believed to be protonated while other acidic and basic residues are to remain at neutral pH, using the Inferred Solvent Condition is the appropriate approach. Note that all essential hydrogens must be present in the entire model, not just in the "special" residues.
Polar Proximity: option menu: {Off|Via_Bond|Through_Space}; This option menu is only active if the "Calculate" method is chosen. When two or more polar groups are in "in proximity" within a molecule, their effects are cumulatively diminished -- this is termed the polar proximity effect and is dealt with by the Leo method of LogP estimation and by HINT as corrective factors to the hydrophobic atom constants. HINT offers three options for Polar Proximity: "Off", "Via_Bond", and "Through_Space". The Via_Bond method is most compatible with the Leo system, and is the option recommended. Through_Space may be appropriate for some larger molecules that have significant intramolecular non-covalent interactions between polar groups. It uses a through-space distance function to estimate the polar proximity effect.
Through Space Function...: push button; This button, which is only active if Polar Proximity is chosen to be Through_Space, calls the Polar Prox. Dist. dialog to define the specific through-space distance function to be applied to the polar proximity correction.