Method, system, and computer program for displaying chemical data

• US 7,188,055 B2
• Filed: 03/12/2001
• Issued: 03/06/2007
• Est. Priority Date: 11/04/1996
• Status: Expired due to Fees

• Current Assignee: Johnson & Johnson Pharmaceutical Research & Development LLC (Johnson & Johnson)
• Original Assignee: Johnson & Johnson Pharmaceutical Research & Development LLC (Johnson & Johnson)
• Inventors: Agrafiotis, Dimitris K, Salemme, Francis R, Lobanov, Victor S
• Primary Examiner(s): PHAN, THAI Q
• Application Number:
  US09/802,956
• Publication Number:
  US 20020069043A1
• Time in Patent Office: 2,185 Days
• Field of Search: 703/2, 703/12, 702 27- 28, 702 30- 32, 702/179, 702/186, 702/181, 702/22, 382/154, 382/165, 382/224
• US Class Current: 703/2
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: G06F 18/2137 based on criteria of topology preservation, e.g. multidimensional scaling or self-organising maps
• CPC Class Codes: G06F 18/40 Software arrangements specially adapted for pattern recognition, e.g. user interfaces or toolboxes therefor
• CPC Class Codes: G06T 11/206 Drawing of charts or graphs
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry
• CPC Class Codes: G16C 20/70 Machine learning, data mining or chemometrics
• CPC Class Codes: G16C 20/80 Data visualisation

Abstract

A system, method, and computer program product for visualizing and interactively analyzing data relating to chemical compounds. A user selects a plurality of compounds to map, and also selects a method for evaluating similarity/dissimilarity between the selected compounds. A non-linear map is generated in accordance with the selected compounds and the selected method. The non-linear map has a point for each of the selected compounds, wherein a distance between any two points is representative of similarity/dissimilarity between the corresponding compounds. A portion of the non-linear map is then displayed. Users are enabled to interactively analyze compounds represented in the non-linear map.

Claims

1. A method for graphically interfacing between a computer system and a user, wherein the computer system interactively displays objects representative of chemical compounds, wherein distances between the objects represent dissimilarity between the corresponding chemical compounds, comprising:

(1) receiving a user selected list of chemical compounds;

(2) displaying objects representative of the user-selected chemical compounds in a window of a display screen, wherein distances between the objects represent dissimilarity between the corresponding chemical compounds;

(3) receiving user input relating to one or more of the following;

(i) deleting one or more of the objects from the window;

(ii) adding one or more additional objects to the window;

(iii) displaying chemical compound information associated with one or more of the objects;

(iv) selecting between having the computer system evaluate the dissimilarities or retrieve dissimilarity values from a source;

(v) selecting one or more dissimilarity evaluation techniques;

(vi) selecting one or more properties to be evaluated as part of a dissimilarity evaluation;

(vii) selecting a scaling factor for one or more of the properties.

2. The method according to claim 1, further comprising:

(4) repeating steps (1) through (3) for a second user-selected list of chemical compounds, wherein objects representative of the second user-selected chemical compounds are displayed in the window.

3. The method according to claim 1, further comprising:

(4) repeating steps (1) through (3) for a second user-selected list of chemical compounds, wherein objects representative of the second user-selected chemical compounds are displayed in a second window.

4. The method according to claim 1, wherein step (3) further comprises receiving user input relating to one or more of the following:

(viii) dragging one or more objects from the first window to a second window of the display screen; and

(ix) dragging one or more objects to the first window from the second window.

5. The method according to claim 1, wherein step (3) further comprises receiving user input relating to one or more of the following:

(viii) selecting one or more of the objects; and

(ix) selecting one or more types of information related to the associated chemical compounds to be displayed.

6. The method according to claim 5, wherein the one or more types of information include one or more selected from:

chemical compound information;

active site docker information; and

nuclear magnetic resonance information.

7. The method according to claim 1, wherein step (3) further comprises receiving user input relating to one or more of the following:

(viii) selecting one or more areas of the window; and

(ix) selecting one or more types of information related to the associated chemical compounds to be displayed.

8. The method according to claim 7, wherein the one or more types of information include one or more selected from:

chemical compound information;

active site docker information; and

nuclear magnetic resonance information.

9. The method according to claim 1, wherein step (3) further comprises receiving user input relating to one or more of the following:

(viii) setting a number of dimensions represented in the window;

(ix) manipulating an orientation of the window;

(x) manipulating a zooming function associate with the window; and

(xi) manipulating one or more appearance features of one or more of the objects.

10. The method according to claim 9, wherein said manipulating an orientation of the window comprises manipulation one or more of rotation, resizing, and translation.

11. The method according to claim 9, wherein the one or more appearance features comprise one or more selected from:

size;

shape;

color;

intensity of color;

degree of visibility;

degree of transparency; and

degree of shininess.

12. The method according to claim 11, wherein the one or more appearance features represent one or more of the following:

a physical feature of the corresponding chemical compound;

a chemical feature of the corresponding chemical compound;

a biological feature of the corresponding chemical compound;

a cost of the corresponding chemical compound;

a difficulty of synthesizing of the corresponding chemical compound; and

an availability of the corresponding compound.

13. The method according to claim 1, wherein step (3) further comprises receiving user input relating to one or more of the following:

(a) changing positions of one or more of the objects; and

(b) changing relationships between two or more of the objects.

14. The method according to claim 1, further comprising displaying multiple sets of objects on the window, wherein step (3) further comprises receiving user input commanding the computer system to toggle between the multiple sets of objects.

15. The method according to claim 1, wherein step (1) comprises allowing the user to drag a set of one or more selected compounds from a second window into the first window.

16. The method according to claim 1, wherein step (1) comprises allowing the user to select the list of chemical compounds from a structure browser window.

17. The method according to claim 1, wherein step (1) comprises allowing the user to type the list of chemical compounds.

18. The method according to claim 1, wherein step (1) comprises allowing the user to select building blocks, wherein the computer system generates a combinatorial library of chemical compounds from the user-selected building blocks.

19. The method according to claim 1, further comprising:

(4) Displaying a structure browse window, said structure browser window including a plurality user-selectable tabbed pages, each said user-selectable tabbed page associated with a set of chemical compounds or a library, wherein each said library tab is associated with a second set of tabbed pages corresponding to building blocks associated with the corresponding library, wherein the user can select one or more chemical compounds and/or de-select one or more chemical compounds and/or one or more building blocks for display in the window.

20. A computer program product comprising a computer useable medium having computer program logic stored therein, said computer program logic enabling a computer system to graphically interface with one or more users to interactively display information related to chemical compounds, wherein said computer program logic comprises:

(a) a compound selection function that enables the computer system to receive a user-selected list of chemical compounds;

(b) a displaying function that enables the computer system to display objects representative of the user-selected chemical compounds in a window of a display screen, wherein distances between the objects represent dissimilarity between the corresponding chemical compounds; and

(c) a user-input function that enables the computer system to receive user input relating to one or more of the following;

(i) deleting one or more of the objects from the window;

(ii) adding one or more additional objects to the window; and

(iii) displaying chemical compound information associated with one or more of the objects;

(iv) selecting between having the computer system evaluate the dissimilarities or retrieve dissimilarity values from a source;

(v) selecting one or more dissimilarity evaluation techniques;

(vi) selecting one or more properties to be evaluated as part of a dissimilarity evaluation;

(vii) selecting a scaling factor for one or more of the properties.