An example HASL creation and testing session is presented herein to illustrate the steps in detail. This example uses 15 glutamine synthetase inhibitor structures (see Theory; Phosphorus and Sulfur, 45, 183, 1989) in the Alchemy *.MOL format. The files containing these structures are located in the subdirectory, "DATA," on the HASL program diskette. These structures were superposed in a prior step to maximize steric overlap of the CH2CH2CH(NH2)COOH backbone, and segregated into a 10-member learning set and a 5-member test set:
Learning Set
Molecule Structure pKi GS3 (HO)2POCH2PO(OH)CH2CH2CH(NH2)COOH 3.60 GS4 CH3PO(OH)CH2CH2CH(NH2)COOH 4.14 GS6 (HO)2P(O)CH2COCH2CH2CH(NH2)COOH 3.23 GS7 CH3CH2SO(NH)CH2CH2CH(NH2)COOH 1.66 GS9 HOPH(O)CH2CH2CH(NH2)COOH 2.68 GS10 HOOCCH2PO(OH)CH2CH2CH(NH2)COOH 2.14 GS12 3,4-Cl2PhCH2PO(OH)CH2CH2CH(NH2)COOH 1.81 GS13 3,5-(CH3)2PhCH2PO(OH)CH2CH2CH(NH2)COOH 1.81 GS17 HONHCH2CH2CH(NH2)COOH 4.68 GS19 Tetrazolyl-CH2CH2CH(NH2)COOH 2.68Test Set
/Molecule Structure pKi GS5 CH3SO(NH)CH2CH2CH(NH2)COOH 3.79 GS11 PhCH2PO(OH)CH2CH2CH(NH2)COOH 2.14 GS14 4-BrPhCH2PO(OH)CH2CH2CH(NH2)COOH 1.81 GS20 HOOCC(=CH2)CH2CH(NH2)COOH 2.66 GS27 Tabtoxinine-b-lactam 3.00The selection of the learning and test set members do not necessarily reflect the best possible modeling paradigm; the sets were chosen at random and serve simply to illustrate HASL model building and testing.
Using the HASL Options Menu
The parameter file, PARAMS.DAT, was edited using the Parameter screen to opt for the default atom types (as listed), lattice resolution at 2.5 Angs, rotational increment (default value), fitting method (eqn 1), file format (Alchemy MOLFILE), fitting method (fixed), and H-value definition (normal). The options then selected were:
Create HASL and Test Molecule(s) Both operations in one session 10 10-member learning set file name (e.g. data\gs3.mol) File name/activity values are entered activity (e.g. 3.60) for all 10 molecules in the learning set new History file Starting a new HASL model 300 iterations Arbitrary choice 0.001 error limit Even if the error limit is not achieved, the iteration process minimizes the error 5 5-member test set file name & activity (as above) Test set data entered for all 5 moleculesAt this point the HASL program creates a batch file (SERIES.BAT) to carry out the above instructions, shells out to DOS, launches the batch file, and upon its completion, returns the user to the Options Menu. The commands listed below are those found in the SERIES.BAT batch file:
create<mol1.fit the first molecule becomes a lattice of points, a HASL fit<mol2.fit the second molecule is "fitted" onto the lattice merge the first and second molecular lattices are merged into one HASL fit<mol3.fit the third molecule is "fitted" onto the merged lattice merge the HASL incorporates new points from the third molecule fit<mol4.fit ...and so on ... merge fit<mol5.fit merge fit<mol6.fit merge fit<mol7.fit merge fit<mol8.fit merge fit<mol9.fit merge fit<mol10.fit merge copy history.000 history after all ten molecular lattices have been merged, the fit<mol1.fit history file is nulled and molecules 1-10 are re-fitted fit<mol2.fit onto the 10-molecule HASL; in this way, the history fit<mol3.fit file accurately records the points in the HASL which fit<mol4.fit belong to each molecule fit<mol5.fit fit<mol6.fit fit<mol7.fit fit<mol8.fit fit<mol9.fit fit<mol10.fit iterations are run according to the itlim file contents & iterate the best receptor description is written to RECEPTOR copy history.000 history new history file to record test molecule fitting fit<mol1.tst each test molecule is fitted unto the iterated HASL fit<mol2.tst fit<mol3.tst fit<mol4.tst fit<mol5.tst
All the molecular coordinate file names and activity values are stored in either MOL*.FIT (learning set members) or MOL*.TST (test set members) files. Both file sets have the same format, for example, in this case MOL1.FIT contains the following two lines:
When CREATE.EXE is run in the batch mode, as the command line,
create
As stated earlier, the information in ITERAT.DAT (list of actual and predicted learning set
activity values) makes up the Learning Set Report (see Reports), while the HISTORY file
contains the information necessary to construct the Test Set Report. Please note that these
reports are necessarily volatile (i.e. subject to change depending on any further user-initiated
building and testing of the HASL model).
In the present case, if the user wishes to add the 5-member test set to the HASL model
(thus creating a 15 molecule HASL model), when "Create HASL" is next chosen from the Options
Menu, and no other operations have been performed, the user can elect to "Add to the Current
HASL," and follow ensuing prompts.
Batch File Operations
The HASL suite of programs, namely, CREATE, FIT AND MERGE, were designed to be called in a logical sequence in order to permit the user the greatest degree of flexibility in designing a modeling paradigm. Thus, the use of batch file mode to explore alternative ways of creating a HASL model is encouraged.