Method, system, and computer program product for...

Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Chemical

Reexamination Certificate

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C703S002000, C702S027000, C702S028000, C702S030000, C702S031000, C702S032000, C702S179000, C702S180000, C702S181000

Reexamination Certificate

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06295514

ABSTRACT:

BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention is generally directed to displaying and processing data using a computer, and more particularly directed to visualizing and interactive processing chemical compounds using a computer.
2. Related Art
Currently, research to identify chemical compounds with useful properties (such as paints, finishes, plasticizers, surfactants, scents, drugs, herbicides, pesticides, veterinary products, etc.) often includes the synthesis/acquisition and analysis of large libraries of chemical compounds. More and more, combinatorial chemical libraries are being synthesized/acquired and analyzed to conduct this research.
A combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical “building blocks” such as reagents. For example. a linear combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds theoretically can be synthesized through such combinatorial mixing of chemical building blocks. For example, one commentator has observed that the systematic, combinatorial mixing of 100 interchangeable chemical building blocks results in the theoretical synthesis of 100 million tetrameric compounds or 10 billion pentameric compounds (Gallop et al., “Applications of Combinatorial Technologies to Drug Discovery, Background and Peptide Combinatorial Libraries, ” J. Med. Chem. 37, 1233-1250 (1994)).
Advanced research in this area often involves the use of directed diversity 486 libraries. A directed diversity library is a large collection of chemical compounds having properties/features/characteristics that match some prescribed properties. The generation, analysis, and processing of directed diversity libraries are described in U.S. Pat. Nos. 5,463,564; 5,574,656; and 5,684,711, and pending U.S. application titled “SYSTEM, METHOD AND COMPUTER PROGRAM PRODUCT FOR IDENTIFYING CHEMICAL COMPOUNDS HAVING DESIRED PROPERTIES,” all of which are herein incorporated by reference in their entireties.
In conducting such research, it would be very valuable to be able to compare the properties, features, and other identifying characteristics of compounds. For example, suppose that a researcher has identified a compound X that exhibits some useful properties. It would aid the researcher greatly if he could identity similar compounds, since those similar compounds might also exhibit those same useful properties.
It would also help a researcher in his work to be able to easily synthesize compounds, or retrieve compounds from a chemical inventory. Further, it would greatly aid a researcher to be able to interactively analyze and otherwise process chemical compounds.
SUMMARY OF THE INVENTION
Briefly stated, the present invention is directed to a system method, and computer program product for visualizing and interactively analyzing data relating to chemical compounds. The invention operates as follows. 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.
Further features and advantages of the present invention, as well as the structure and operation of various embodiments of the present inventions are described in detail below with reference to the accompanying drawings. In the drawings, like reference numbers indicate identical or functionally similar elements. Also, the leftmost digit(s) of the reference numbers identify the drawings in which the associated elements are first introduced.


REFERENCES:
patent: 4773099 (1988-09-01), Bokser
patent: 4811217 (1989-03-01), Tokizane et al.
patent: 4859736 (1989-08-01), Rink
patent: 4908773 (1990-03-01), Pantoliano et al.
patent: 4935875 (1990-06-01), Shah et al.
patent: 4939666 (1990-07-01), Hardman
patent: 5010175 (1991-04-01), Rutter et al.
patent: 5025388 (1991-06-01), Cramer, III et al.
patent: 5155801 (1992-10-01), Lincoln
patent: 5167009 (1992-11-01), Skeirik
patent: 5181259 (1993-01-01), Rorvig
patent: 5240680 (1993-08-01), Zuckerman et al.
patent: 5260882 (1993-11-01), Blanco et al.
patent: 5265030 (1993-11-01), Skolnick et al.
patent: 5270170 (1993-12-01), Schatz et al.
patent: 5288514 (1994-02-01), Ellman
patent: 5307287 (1994-04-01), Cramer, III et al.
patent: 5323471 (1994-06-01), Hayashi
patent: 5331573 (1994-07-01), Balaji et al.
patent: 5434796 (1995-07-01), Weininger
patent: 5436850 (1995-07-01), Eisenberg et al.
patent: 5442122 (1995-08-01), Noda et al.
patent: 5463564 (1995-10-01), Agrafiotis et al.
patent: 5499193 (1996-03-01), Sugawara et al.
patent: 5519635 (1996-05-01), Miyake et al.
patent: 5524065 (1996-06-01), Yagasaki
patent: 5526281 (1996-06-01), Chapman et al.
patent: 5545568 (1996-08-01), Ellman
patent: 5549974 (1996-08-01), Holmes
patent: 5553225 (1996-09-01), Perry
patent: 5565325 (1996-10-01), Blake
patent: 5574656 (1996-11-01), Agrafiotis et al.
patent: 5585277 (1996-12-01), Bowie et al.
patent: 5602755 (1997-02-01), Ashe et al.
patent: 5602938 (1997-02-01), Akiyama et al.
patent: 5612895 (1997-03-01), Balaji et al.
patent: 5634017 (1997-05-01), Mohanty et al.
patent: 5635598 (1997-06-01), Lebl et al.
patent: 5670326 (1997-09-01), Beutel
patent: 5679582 (1997-10-01), Bowie et al.
patent: 5684711 (1997-11-01), Agrafiotis et al.
patent: 5703792 (1997-12-01), Chapman
patent: 5712171 (1998-01-01), Zambias et al.
patent: 5712564 (1998-01-01), Hayosh
patent: 5736412 (1998-04-01), Zambias et al.
patent: 5740326 (1998-04-01), Boulet et al.
patent: 5789160 (1998-08-01), Eaton et al.
patent: 5807754 (1998-09-01), Zambias et al.
patent: 5811241 (1998-09-01), Goodfellow et al.
patent: 5832494 (1998-11-01), Egger et al.
patent: 5858660 (1999-01-01), Eaton et al.
patent: 5861532 (1999-01-01), Brown et al.
patent: 5866334 (1999-02-01), Beutel
patent: 5901069 (1999-05-01), Agrafiotis et al.
patent: 5908960 (1999-06-01), Newlander
patent: 5933819 (1999-08-01), Skolnick et al.
patent: 6014661 (2000-01-01), Ahlberg et al.
patent: 6037135 (2000-03-01), Kubo et al.
patent: 6049797 (2000-04-01), Guha et al.
patent: 0 355 266 B1 (1993-06-01), None
patent: 0 355 628 B1 (1993-11-01), None
patent: 0 770 876 A1 (1997-05-01), None
patent: 0 818 744 A2 (1998-01-01), None
patent: WO 91/19735 (1991-12-01), None
patent: WO 92/00091 (1992-01-01), None
patent: WO 93/20242 (1993-10-01), None
patent: WO 94/28504 (1994-12-01), None
patent: WO 95/01606 (1995-01-01), None
patent: WO 97/09342 (1997-03-01), None
patent: WO 97/20952 (1997-06-01), None
patent: WO 97/27559 (1997-07-01), None
patent: WO 98/20459 (1998-05-01), None
Gasteiger et al, “Assessment of the Diversity of Combinatorial Libraries by an Encoding of Molecular Surface Properties”, Abstracts of Papers, American Chemical Society, 211th ACS National Meeting, Item 070, Mar. 1996.*
Appl. No. 09/303,671 Agrafiotis et al. May 3, 1999.
Appl. No. 08/963,870 Agrafiotis et al. Nov. 4, 1997.
Appl. No. 09/073,845 Agrafiotis et al. May, 7, 1998.
Borg, Inger and Groenen, Patrick,Modern Multidimensional Scaling Theory and Applications,Springer Series in Statistics, 1997, entire book submitted.
Agrafiotis, D.K. et al., “Advances in diversity profiling and combinatorial series design,”Molecular Diversity,vol. 4, 1999, pp. 1-22.
Agrafiotis, D.K. and Lobanov, V.S., “An Efficient Implementation of Distance-Based Diveristy Measure based on k-d Trees,”J. Chem. Inf. Comput. Sci.,vol. 39, No. 1, Jan./Feb. 1999, pp. 51-58.
Agrafiotis,

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