Method of analyzing , organizing and visualizing chemical data with feature hierarchy

Abstract

The present invention is directed to a method and system for displaying correlations between structural Features of a molecule and the biological or physical properties of the molecule. A unique feature of the present invention is that the user has a convenient way to select and explore a succession of interesting subsets and to interactively control the contents of each subset using filters. The medicinal chemist can thereby use his or her intuition and experience to guide the process of drug selection. In a preferred embodiment, the method and system of the invention uses at least four coordinating panels which comprise: 1) one or more first panels containing a series of molecular structural Feature or ranges of properties, such as molecular weight; 2) a second panel showing a graph (e.g., a bar graph) of the contents of the set shown in the first panel, the size of the bar graph may represent the number of members of the set containing the Feature or the biological or physical property of the set; 3) a third panel containing at least one interactive control, i.e. a two-ended slider, wherein each control corresponds to a biological or physical property of the set; and 4) a fourth panel for selecting and adjusting the graphical display of the biological or physical property displayed in the second panel.

We claim:  
     
         1 . A method for analyzing sets of compounds comprising: 
 compiling chemical resources comprising templates representing structural features for a plurality of compounds;    storing said compiled chemical resources;    selecting a plurality of compounds from said stored compiled chemical resources according to structural features defined in said templates;    determining biological data and physical property data for said plurality of compounds selected from said stored compiled chemical resources;    storing said biological data and physical property data for said plurality of compounds;    selecting at least one structural feature associated with said plurality of compounds for said stored biological data and physical property data; and    displaying a representation of the members of a set comprising compounds from said plurality of compounds for said stored biological data and physical property data, said members selected in accordance with said at least one structural feature.    
     
     
         2 . The method of  claim 1  wherein said structural features comprise atoms and bonds.  
     
     
         3 . The method of  claim 1  wherein said biological data comprises a biological response variable.  
     
     
         4 . The method of  claim 1  wherein said physical property data comprises values for molecular weight, the number of rotatable bonds, the number of hydrogen bond donors, and the number of hydrogen bond acceptors.  
     
     
         5 . The method of  claim 1  wherein selecting at least one structural feature comprises selecting a structural feature identified by name.  
     
     
         6 . The method of  claim 1  wherein selecting at least one structural feature comprises selecting a structural feature identified by a chemical diagram.  
     
     
         7 . The method of  claim 1  further comprising displaying a representation of the members of a set comprising compounds from said plurality of compounds for said stored biological data and physical property data, said members selected in accordance with said physical property data.  
     
     
         8 . The method of  claim 7  further comprising: 
 adjusting a value associated with said physical property data; and  
 displaying a representation of the members of a set comprising compounds from said plurality of compounds for said stored biological data and physical property data, said members selected in accordance with said adjusted physical property data or biological response data.  
 
     
     
         9 . A system for analyzing sets of compounds comprising: 
 a first data store, said first data store comprising compiled chemical resources comprising templates representing structural features for a plurality of compounds;    a second data store, said second data store comprising biological data and physical property data for said plurality of compounds selected from said first data store according to structural features defined in said templates;    a third data store, said third data store comprising a subset of said plurality of compounds selected according to said structural features and said biological data or said physical property data;    a server for retrieving data from said third data store in accordance with client requests; and    a client for displaying a representation of the members of a set comprising compounds from said third data store, said members selected from said third data store by said server in accordance with a client request comprising at least one structural feature and a value associated with said biological data or said physical property data.    
     
     
         10 . The system of  claim 9  wherein said structural features comprise atoms and bonds.  
     
     
         11 . The system of  claim 9  wherein said biological data comprises a biological response variable.  
     
     
         12 . The system of  claim 9  wherein said physical property data comprises values for molecular weight, the number of rotatable bonds, the number of hydrogen bond donors, and the number of hydrogen bond acceptors.  
     
     
         13 . The system of  claim 9  wherein said client request comprising at least one structural feature comprises a structural feature identified by name.  
     
     
         14 . The system of  claim 9  wherein said client request comprising at least one structural feature comprises a structural feature identified by a chemical diagram.  
     
     
         15 . The system of  claim 9  wherein said graphical representation is a histogram.  
     
     
         16 . A method in a computer system for analyzing data for a set of compounds selected in accordance with structural features comprising: 
 displaying in a first panel structural features of compounds;    displaying in a second panel a representation of a set of compounds selected in accordance with said structural features in said first panel; and    displaying in a third panel at least one interactive control that allows a user to adjust the members of said set of compounds selected in accordance with said structural features in said first panel.    
     
     
         17 . The method of  claim 16  wherein displaying said structural features in said first panel comprises displaying a list of names for structural classes.  
     
     
         18 . The method of  claim 17  wherein said names for said structural classes are selected from the group consisting of amino acids, bases, nucleosides, benzenes, carbocycles, carbohydrates, carbon chains, functional groups, heterocycles, linker groups, naphthalenes, natural products, pharmacophores, and toxic, reactive groups.  
     
     
         19 . The method of  claim 16  wherein displaying in a second panel a representation of a set of compounds selected in accordance with said structural features in said first panel comprises displaying histogram bars wherein the length of each histogram bar represents the number of members of the set with the selected structural feature.  
     
     
         20 . The method of  claim 16  further comprising displaying in said first panel biological or physical properties for a plurality of compounds.  
     
     
         21 . The method of  claim 20  further comprising displaying in said second panel a representation of a set of compounds selected in accordance with said biological or physical properties selected from said first panel.  
     
     
         22 . The method of  claim 21  wherein displaying in a second panel a representation of a set of compounds selected in accordance with said biological or physical properties comprises displaying histogram bars wherein the length of each histogram bar represents the number of members of the set with the selected biological or physical property.  
     
     
         23 . The method of  claim 20  wherein said biological properties comprise biological response variables.  
     
     
         24 . The method of  claim 20  wherein said physical properties comprise values for molecular weight, the number of rotatable bonds, the number of hydrogen bond donors, and the number of hydrogen bond acceptors.  
     
     
         25 . The method of  claim 16  wherein displaying in a second panel a representation of a set of compounds selected in accordance with said structural features in said first panel comprises displaying a scatterplot.