PROCESS FOR IDENTIFYING SIMILAR 3D SUBSTRUCTURES ONTO 3D ATOMIC STRUCTURES AND ITS APPLICATIONS
First Claim
1. A computer-implemented process for identifying and displaying 3D atomic substructures on a 3D atomic structure of a first macromolecule having a plurality of individual atoms comprising:
- a) providing a programmed computer which performs steps (b)-(j) using a microprocessor and a computer visual display;
b) attributing to each individual atom of a 3D atomic structure of a macromolecule a structural parameter combining atomic local density D, local center of mass C and orientation in relation to position P;
c) constructing chemical groups by setting individual atoms of a macromolecule having similar structural parameters;
d) constructing clusters of at least three chemical groups of a macromolecule by setting the chemical groups whose reciprocal distances are constrained;
e) constructing an input graph of the clusters constructed in step (d);
f) for a set of individual macromolecules, storing the constructed clusters and the corresponding input graphs in a reference computer database;
g) using the programmed computer to compare clusters constructed in step (d) and the input graph constructed in step (e) for a first macromolecule, to the clusters constructed in step (d) and the input graph constructed in step (e) for the set of individual macromolecules stored in the reference computer database constructed in step (f);
h) identifying a similar 3D atomic substructure on the first macromolecule with the programmed computer by recognizing the clusters of the first macromolecule sharing similar 3D atomic substructures with the clusters of the individual macromolecules in the set stored in the reference computer database;
i) determining with the programmed computer a functional 3D atomic substructure on the first macromolecule by correlating the similar 3D atomic substructure on the first macromolecule with a known biochemical activity of a similar 3D atomic substructure in an individual macromolecule of the set stored in the reference computer database; and
j) displaying a visual representation of the determined functional 3D atomic substructure on the first macromolecule on the computer visual display;
whereby a 3D atomic substructure on a 3D atomic structure of a first macromolecule having a plurality of individual atoms is identified and displayed.
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Accused Products
Abstract
Our disclosure pertains to the field of structural biology and relates to a process to compare various three-dimensional (3D) structures and to identify functional similarities among them. Our process of comparison of 3D atomic structures is based on the comparisons of defined chemical groups onto the 3D atomic structures and allows the detection of local similarities even when neither the fold nor sequence for example aminoacid sequences for polypeptides sequences or nucleotide sequences for nucleic acid sequences are conserved. This process requires the attribution of selected physico-chemical parameters to each atom of a 3D atomic structure, then the representation of each 3D atomic structure by a graph of chemical groups.
5 Citations
30 Claims
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1. A computer-implemented process for identifying and displaying 3D atomic substructures on a 3D atomic structure of a first macromolecule having a plurality of individual atoms comprising:
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a) providing a programmed computer which performs steps (b)-(j) using a microprocessor and a computer visual display; b) attributing to each individual atom of a 3D atomic structure of a macromolecule a structural parameter combining atomic local density D, local center of mass C and orientation in relation to position P; c) constructing chemical groups by setting individual atoms of a macromolecule having similar structural parameters; d) constructing clusters of at least three chemical groups of a macromolecule by setting the chemical groups whose reciprocal distances are constrained; e) constructing an input graph of the clusters constructed in step (d); f) for a set of individual macromolecules, storing the constructed clusters and the corresponding input graphs in a reference computer database; g) using the programmed computer to compare clusters constructed in step (d) and the input graph constructed in step (e) for a first macromolecule, to the clusters constructed in step (d) and the input graph constructed in step (e) for the set of individual macromolecules stored in the reference computer database constructed in step (f); h) identifying a similar 3D atomic substructure on the first macromolecule with the programmed computer by recognizing the clusters of the first macromolecule sharing similar 3D atomic substructures with the clusters of the individual macromolecules in the set stored in the reference computer database; i) determining with the programmed computer a functional 3D atomic substructure on the first macromolecule by correlating the similar 3D atomic substructure on the first macromolecule with a known biochemical activity of a similar 3D atomic substructure in an individual macromolecule of the set stored in the reference computer database; and j) displaying a visual representation of the determined functional 3D atomic substructure on the first macromolecule on the computer visual display; whereby a 3D atomic substructure on a 3D atomic structure of a first macromolecule having a plurality of individual atoms is identified and displayed. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
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27. A computer-implemented method for identifying and displaying 3D atomic substructures on a 3D atomic structure of a first macromolecule having a plurality of individual atoms comprising:
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a) providing a first programmed computing device which performs steps (b)-(f) and (i)-(l) using a microprocessor connected to a computer visual display device, a second programmed computing device which performs step (g) using a microprocessor and comprises a reference database, and a connection for communication between the first computing device and the second computing device; b) attributing on the first computing device to each individual atom of a 3D atomic structure of a macromolecule a structural parameter combining atomic local density D, local center of mass C and orientation in relation to position P; c) constructing on the first computing device chemical groups by setting individual atoms of a macromolecule having similar structural parameters; d) constructing on the first computing device clusters of at least three chemical groups of a macromolecule by setting the chemical groups whose reciprocal distances are constrained; e) constructing on the first computing device an input graph of the clusters constructed in step (d); f) sending via the connection the constructed clusters and the corresponding input graphs for a set of individual macromolecules from the first computing device to the second computing device; g) storing the constructed clusters and the corresponding input graphs in the reference computer database of the second computing device; h) delivering to the first computing device the constructed clusters and the corresponding input graphs from the reference computer database of the second computing device via the connection; i) comparing on the first computing device the clusters constructed in step (d) and the input graph constructed in step (e) for a first macromolecule, to the clusters constructed in step (d) and the input graph constructed in step (e) for the set of individual macromolecules stored in the reference computer database constructed of the second computing device in step (g); j) identifying on the first computing device a similar 3D atomic substructure on the first macromolecule by recognizing the clusters of the first macromolecule sharing similar 3D atomic substructures with the clusters of the individual macromolecules in the set retrieved from the reference computer database of the second computing device; k) determining on the first computing device a functional 3D atomic substructure on the first macromolecule by correlating the similar 3D atomic substructure on the first macromolecule with a known biochemical activity of a similar 3D atomic substructure in an individual macromolecule of the set stored in the reference computer database on the second computing device; and l) displaying on the computer visual display device of the first computing device a visual representation of the determined functional 3D atomic substructure on the first macromolecule; whereby a 3D atomic substructure on a 3D atomic structure of a first macromolecule having a plurality of individual atoms is identified and displayed.
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28. A computer program product, comprising a computer usable medium having a computer readable program code embodied therein, said computer readable program code adapted to be executed to implement a method for generating a report or visual display, said method comprising:
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a) providing a system, wherein the system comprises distinct software modules and a computer visual display device, and wherein the distinct software modules comprise a construction module, a graphing module, a storage module, a comparison module, an identification module, a determination module and a data display module; b) attributing to each individual atom of a 3D atomic structure of a macromolecule a structural parameter combining atomic local density D, local center of mass C and orientation in relation to position P with the construction module; c) constructing chemical groups by setting individual atoms of a macromolecule having similar structural parameters with the construction module; d) constructing clusters of at least three chemical groups of a macromolecule by setting the chemical groups whose reciprocal distances are constrained with the construction module; e) constructing an input graph of the clusters constructed in step (d) with the graphing module; f) storing the constructed clusters and the corresponding input graphs for a set of individual macromolecules with the storage module; g) comparing with the comparison module the clusters constructed in step (d) and the input graph constructed in step (e) for a first macromolecule, to the clusters constructed in step (d) and the input graph constructed in step (e) for the set of individual macromolecules stored by the storage module in step (f); h) identifying with the identification module a similar 3D atomic substructure on the first macromolecule by recognizing the clusters of the first macromolecule sharing similar 3D atomic substructures with the clusters of the individual macromolecules stored by the storage module in step (f); i) determining with the determination module a functional 3D atomic substructure on the first macromolecule by correlating the similar 3D atomic substructure on the first macromolecule with a known biochemical activity of a similar 3D atomic substructure in an individual macromolecule of the set stored by the storage module in step (f); and j) displaying on the computer visual display device a report or visual representation of the determined functional 3D atomic substructure on the first macromolecule with the display module.
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29. A computer-implemented process for identifying and displaying 3D atomic substructures on a 3D atomic structure of a first macromolecule having a plurality of individual atoms comprising:
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a) providing a programmed computer which performs steps (c)-(j) using a microprocessor that executes multiple arithmetic operations to evaluate complex mathematical expressions during a comparison of 3D macromolecular substructures; b) providing a computer visual display to optionally visualize any detected correlation of similar 3D atomic substructures; c) attributing to each individual atom of a 3D atomic structure of a macromolecule a structural parameter combining atomic local density D, local center of mass C and orientation in relation to position P; d) constructing chemical groups by setting individual atoms of a macromolecule having similar structural parameters; e) constructing clusters of at least three chemical groups of a macromolecule by setting the chemical groups whose reciprocal distances are constrained; f) constructing an input graph of the clusters constructed in step (e); g) for a set of individual macromolecules, storing the constructed clusters and the corresponding input graphs of the set in a reference computer database to organize information in a suitable form for deleting records, adding new entries or searching for a specific input graph; h) using the programmed computer to compare the clusters constructed in step (e) and the input graph constructed in step (f) for a first macromolecule, to the clusters constructed in step (e) and the input graph constructed in step (f) for the set of individual macromolecules stored in the reference computer database constructed in step (g); i) identifying a similar 3D atomic substructure on the first macromolecule with the programmed computer by recognizing the clusters of the first macromolecule sharing similar 3D atomic substructures with the clusters of the individual macromolecules in the set stored in the reference computer database; j) determining with the programmed computer a functional 3D atomic substructure on the first macromolecule by correlating the similar 3D atomic substructure on the first macromolecule with a known biochemical activity of a similar 3D atomic substructure in an individual macromolecule of the set stored in the reference computer database; and k) displaying a visual representation of the determined functional 3D atomic substructure on the first macromolecule on the computer visual display; whereby a 3D atomic substructure on a 3D atomic structure of a first macromolecule having a plurality of individual atoms is identified and displayed.
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30. A computer-implemented method for identifying and displaying 3D atomic substructures on a 3D atomic structure of a first macromolecule having a plurality of individual atoms comprising:
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a) providing a first programmed computing device which performs steps (c)-(g) and (i)-(m) using a microprocessor that evaluates at least a million individual arithmetic operations per second and evaluates every mathematical expression resulting from a detection of correlation between 3D macromolecular atomic substructure; b) providing a second programmed computing device which performs steps (h)-(i) using a microprocessor connected to a computer visual display device to optionally visualize a two-dimensional plot of any detected correlation between 3D macromolecular atomic substructures;
said second computing device comprising a reference database and a data connection for communication between the first computing device and the second computing device;c) attributing on the first computing device to each individual atom of a 3D atomic structure of a macromolecule a structural parameter combining atomic local density D, local center of mass C and orientation in relation to position P; d) constructing on the first computing device chemical groups by setting individual atoms of a macromolecule having similar structural parameters; e) constructing on the first computing device clusters of at least three chemical groups of a macromolecule by setting the chemical groups whose reciprocal distances are constrained; f) constructing on the first computing device an input graph of the clusters constructed in step (e); g) sending via the connection the constructed clusters and the corresponding input graphs for a set of individual macromolecules from the first computing device to the second computing device; h) storing the constructed clusters and the corresponding input graphs in the reference computer database of the second computing device; i) delivering to the first computing device the constructed clusters and the corresponding input graphs from the reference computer database of the second computing device via the connection; j) comparing on the first computing device the clusters constructed in step (d) and the input graph constructed in step (f) for a first macromolecule, to the clusters constructed in step (c) and the input graph constructed in step (f) for the set of individual macromolecules stored in the reference computer database constructed of the second computing device in step (h); k) identifying on the first computing device a similar 3D atomic substructure on the first macromolecule by recognizing the clusters of the first macromolecule sharing similar 3D atomic substructures with the clusters of the individual macromolecules in the set retrieved from the reference computer database of the second computing device; l) determining on the first computing device a functional 3D atomic substructure on the first macromolecule by correlating the similar 3D atomic substructure on the first macromolecule with a known biochemical activity of a similar 3D atomic substructure in an individual macromolecule of the set stored in the reference computer database on the second computing device; and m) displaying on the computer visual display device of the first computing device a visual representation of the determined functional 3D atomic substructure on the first macromolecule; whereby a 3D atomic substructure on a 3D atomic structure of a first macromolecule having a plurality of individual atoms is identified and displayed.
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Specification