The Graphical Interface


HINT Menubar

Found as Hint under "eslc". The HINT command allows you to calculate LogP for small organic molecules, compute 3D maps of hydropathy and hydropathic interactions, and analyze and quantitate atom-atom interactions in the biological environment. Selection of Hint reveals four submenus: Partition, HintMap, HintTable, and HintQSAR. The first three represent the typical steps of a HINT calculation while the HintQSAR submenu contains some utilities for use with the SYBYL Molecular Spreadsheet.


Partition

The Partition submenu contains commands which setup and perform the LogP atom partitition functions. A molecule's partition is the LogP for octanol/water solubility. This number which has significance on its own for Medicinal Chemistry and drug design is reported by the Partition commands. A typical HINT calculation begins by partitioning one or more molecules to assign HINT interaction parameters to the atoms of the molecules.

The two options in this submenu are Molecule... and SMILES... (Active for HINT2.30Ds Users).

Partition Molecule Dialog Box

The Partition Molecule Dialog Box defines the setup of the partition calculation for a molecule that is currently displayed in SYBYL. There are two Methods of LogP determination used by HINT: "Calculate" using the SYBYL atom types and connection matrices, or "Dictionary" using atom names and predefined HINT parameters for registered substructure types such as amino acid residues. This dialog also assists in the setup of several other parameters for molecule partitioning.

Dialog View View Partition Molecule Dialog Box

SMILES (Hint2.30Ds only)

The Partition SMILES command calculates LogP for octanol/water partitioning (hydrophobicity) for SMILES strings entered from the keyboard or from disk files.

Dialog View View Partition SMILES Dialog

Polar Prox. Dist. Dialog Box

The Polar Prox. Dist. Dialog Box assists in defining a distance function for use with the Through_Space Polar Proximity option for Partitioning. Two Functional Forms with tailorable parameters are available in the Dialog.

Dialog View View Polar Prox. Dist. Dialog Box


HintMap

The HintMap submenu contains the commands to execute the HINT map creation for Molecules, InterMolecular and IntraMolecular interactions, for Complementary species, and to calculate difference maps from two input maps. It also contains the Contour command for contouring HINT (or other) 3D maps. The six options on this submenu are: Molecule..., InterMolecular..., IntraMolecular..., Complement..., Difference..., and Contour...

Map Molecule Dialog Box

The Map Molecule dialog box defines the parameters and molecule necessary for creation of a HINT Hydropathic field grid that maps the 3D hydropathy of the molecule.

Dialog View View Map Molecule Dialog Box

Map IntraMolecular Dialog Box

The Map IntraMolecular Dialog Box sets up and executes a HINT calculation on a single molecule to map the non-covalent interactions within the molecule (e.g., folding).

Dialog View View Map IntraMolecular Dialog Box

Map InterMolecular Dialog Box

The Map InterMolecular Dialog Box sets up and executes a map calculation of the non- covalent interactions between two molecules or subunits. Typical uses would be to map the interactions between a ligand and a receptor, or between two protein subunits.

Dialog View View Map InterMolecular Dialog Box

Map Complement Dialog Box

The Map Complement Dialog Box defines parameters and the molecule for calculating a projected hydropathic map of a unknown "complementary" species based on the structure and hydropathic species of a known species. Another terminology would be to refer to the complementary map as a "key" map if the known species is a receptor.

Dialog View View Map Complement Dialog Box

Map Difference Dialog Box

The Map Difference Dialog Box enables you to calculate the difference (or sum) of two separate HINT (or other) contour files. The Difference between two HINT Molecule maps for two related molecules can be used to determine the areas where hydrophobicity is enhanced, etc. The Difference between two HINT Interaction maps reveal the effects on InterMolecular or IntraMolecular stability of site-directed mutagenesis or other chemical changes on the involved molecule(s). Note that the validity and interpretability of a map difference result is enhanced when the two input maps match closely in terms of region spanned and grid spacing.

Dialog View View Map Difference Dialog Box

Contour Dialog Box

The Map Contour Dialog Box is a convenience utility for contouring and displaying SYBYL (.cnt) contour files.

Dialog View View Map Contour Dialog Box

Region Definition Dialog Box

The Region Definition Dialog Box assists in describing the region in 3D cartesian space that the map calculation should span.

Dialog View View Region Definition Dialog Box

Distance Function Dialog Box

Parameters in the Distance Function Dialog Box control the functional form of the HINT calculation with respect to distance between atoms (for HintTable calculations) or between atoms and grid points (for Map calculations).

Dialog View View Distance Function Dialog Box


HintTable

The HintTable submenu contains the commands to execute the HINT interaction table creation for the InterMolecular and IntraMolecular cases.

The two options on this submenu are: InterMolecular..., and IntraMolecular.

Table IntraMolecular Dialog Box

The Table IntraMolecular Dialog Box sets up and executes a HINT calculation on a single molecule to tabulate and categorize the non-covalent interactions within the molecule (e.g., folding).

Dialog View View Table IntraMolecular Dialog Box

Table InterMolecular Dialog Box

The Table InterMolecular Dialog Box sets up and executes a HINT calculation between two molecules that are interacting in some way with one another. This calculation tabulates and categorizes the non-covalent interactions involved in ligand or substrate binding or protein-protein interactions.

Dialog View View Table InterMolecular Dialog Box

Small Ligand Optimization Dialog Box

The Small Ligand Optimization Dialog Box sets up and runs a calculation that uses the HINT "force field" to optimize the position and orientation of a small ligand such as water in the model.

Dialog View View Small Ligand Optimization Dialog Box


HintQSAR

The HintQSAR submenu contains some utility functions to aid in the use of HINT with the SYBYL QSAR module. Most of the HintQSAR functionality is associated with the SYBYL Molecular Spreadsheet. This will be discussed in the next section.

The three options available in the HintQSAR submenu are Add Hint Score Columns to MSS, Graph HintQSAR... and Fill MSS Cells with HintCoMFA Field.

Add Hint Score Columns to MSS

This option will add the seven HINT Score categories (from InterMolecular HintTable calculations) as columns in an open Molecular Spreadsheet. These seven descriptors of interaction (Hydrogen Bond, Acid-Base, Hydrophobic-Hydrophobic, Acid-Acid, Base-Base, Hydrophobic-Polar and Total) provide a rather complete description of the interactions between two species, typically receptor and ligand. Entering these in the Molecular Spreadsheet, referenced by ligand (Molecule2 by definition), will allow multivariate analysis of the HINT binding data against physical or biological properties of the ligand. The Add Score to Current Spreadsheet option on the Table InterMolecular Dialog Box will place the HINT Score data in the correct column/row of the Spreadsheet at the conclusion of the HINT calculation.

Retrieve HintQSAR Dialog Box

The Retrieve HintQSAR Dialog Box is a convenience function to facilitate creation (for graphing) of the CoMFA coefficients*standard deviation contour maps for PLS runs where the HINT hydropathic field was included. The dialog box enables selection of the desired field information and writes the selected CoMFA fields to scratch disk files. Then these fields are sequentially contoured.

Dialog View View Retrieve HintQSAR Dialog Box

Fill MSS Cells with HintCoMFA Field Dialog Box

This command allows you to fill specified MSS cells with the HintCoMFA field. You may wish to use this option if you are attempting to predict activity of a new compound with a CoMFA model that includes the HINT field.

Dialog View View Fill MSS Cells with HintCoMFA Field Dialog Box


HINT and the Molecular Spreadsheet

HINT provides added functionality to the molecular spreadsheet. Four additional column types are defined by HINT: HINTLOGP, HINTSCORE, HINTMAP and HINTCOMFA. These are available through the Spreadsheet "Autofill" button in the list of column types. Note: Occasionally the HINTCOMFA column type is dropped by the Autofill menu. If this happens, type mss!reset_eslc to the Sybyl> prompt.

HINTLOGP: Add Column (HintLogP) Dialog Box

The Add Column (HintLogP) Dialog Box sets the parameters for filling the cells in a spreadsheet column with the partition coefficients of each molecule (row) in the table.

Dialog View View Add Column (HintLogP) Dialog Box

HINTSCORE: Add Columns Dialog Box

The HINTSCORE: Add Columns Dialog Box sets the parameters for filling the cells in spreadsheet columns with the Table scores for A) docking each ligand (row) of the Spreadsheet with a common (rigid) receptor model; B) docking each conformer of the same ligand (row) with a common (rigid) receptor model; or C) calculating an IntraMolecular Table/Score for each conformer (row) of a molecule in the spreadsheet.

Dialog View View HINTSCORE: Add Columns Dialog Box

HINTMAP: MSS Dialog Box

The HINTMAP: MSS Dialog Box sets the parameters for creating Hint hydropathic property and interaction maps for conformations of a single molecule saved in the Molecular Spreadsheet. Map types supported are: InterMolecular interactions, i.e., between a rigid Receptor and the ligand; IntraMolecular interactions; Molecule property, and Complement (presumed interacting species) property. These options may be useful in visualizing molecular structure in response to, for example, dynamics. The filename and relevant map parameters (maximum, minimum, mean) for the created map(s) are stored in columns of the MSS as this calculation proceeds.

Dialog View View HINTMAP: MSS Dialog Box

HINTCOMFA: Add Column (HintCoMFA) Dialog Box

The Add Column (HintCoMFA) Dialog Box sets the parameters for filling each cell in a spreadsheet with the HINT hydropathic field. This Dialog Box contains parameters related to the initial Partitioning of each molecule and parameters related to the HINT map creation for each molecule (row) in the table.

Dialog View View Add Column (HintCoMFA) Dialog Box

Calculate CoMFA Region Automatically Dialog Box

This dialog box is called from the HINT COMFA routine and is used to set the parameters for defining the CoMFA region based on the union space spanned by the entire molecule set. The routine determines the spatial extents of each molecule and creates a region that encompasses all molecules.

Dialog View View Calculate CoMFA Region Automatically Dialog Box

Define CoMFA Region Dialog Box

The Define CoMFA Region Dialog Box is used if the cartesian coordinate set defining the region (Lower Box Corner, Upper Box Corner) is known, or if a custom region that includes more than one Box is needed. This latter case may be a useful option for some CoMFA experiments where much of the molecular structures are identical and a "closeup" on the areas of difference is appropriate.

Dialog View View Define CoMFA Region Dialog Box