SYSTEM AND METHOD FOR MODELLING A MOLECULE WITH A GRAPH
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Abstract
Modelling a molecule by means of a graph, said graph comprising vertices and edges, each edge having a specific type, and said graph having cyclic orderings on the half-edges about at least one of the vertices, said system comprising means for determining the cyclic orderings on the half-edges about said at least one vertex by means of the spatial coordinates of the constituent atoms of the molecule, and means for determining the type of each edge of the graph by means of the relative spatial location of the constituent atoms of the molecule. Thereby automatic classification, comparison, specification, analysis and/or prediction of molecular structures can be provided because these molecular structures are represented by explicit combinatorial objects, and descriptors can be derived from the graph constructed in this manner. The descriptors are automatically computable from molecular databases, such as PDB or CATH, with no qualitative human intervention or subjective criteria. The invention can be applied to macromolecular structures such as proteins, protein globules, ligands, polymers, nucleotides, nucleic acids, RNA and DNA.
9 Citations
72 Claims
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1-39. -39. (canceled)
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40. A method for providing a model of a molecule by means of a graph, comprising the steps of:
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a) providing a graph, said graph comprising vertices and edges, each edge having a specific type, and said graph having cyclic orderings on the half-edges about at least one of the vertices, b) obtaining the spatial coordinates and the relative spatial location of the constituent atoms of the molecule, c) determining cyclic orderings on the half-edges about said at least one vertex by means of the spatial coordinates of the constituent atoms of the molecule, d) determining the type of each edge of the graph by means of the relative spatial location of the constituent atoms of the molecule, and e) modeling the molecule by the resulting graph. - View Dependent Claims (41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59)
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60. A system for providing a model of a molecule by means of a graph, said system comprising:
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a graph comprising vertices and edges, each edge having a specific type, and said graph having cyclic orderings on the half-edges about at least one of the vertices, means for obtaining the spatial coordinates and the relative spatial location of the constituent atoms of the molecule, means for determining cyclic orderings on the half-edges about said at least one vertex by means of the spatial coordinates of the constituent atoms of the molecule, means for determining the type of each edge of the graph by means of the relative spatial location of the constituent atoms of the molecule, and means for modelling the molecule by the resulting graph. - View Dependent Claims (61, 62, 63, 64, 65, 66, 67, 68, 69, 70)
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71. A computer usable medium having computer-readable program code means providing a system for providing a model of a molecule by means of a graph, said graph comprising vertices and edges, each edge having a specific type, and said graph having cyclic orderings on the half-edges about at least one of the vertices, said computer-readable program code comprising:
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computer program code means for obtaining the spatial coordinates and the relative spatial location of the constituent atoms of the molecule, computer program code means for determining cyclic orderings on the half-edges about said at least one vertex by means of the spatial coordinates of the constituent atoms of the molecule, computer program code means for determining the type of each edge of the graph by means of the relative spatial location of the constituent atoms of the molecule, and computer program code means for modelling the molecule by the resulting graph.
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72. A method for providing a model of a peptide unit, said model comprising a horizontal line segment representing the carbon—
- nitrogen bond and a vertical line segment attached on each side of the horizontal line segment, the first and leftmost vertical line segment representing an oxygen site, wherein the relative position of the first and leftmost vertical line segment corresponds to the location of the oxygen atom on the backbone of the peptide unit when traversed in its natural orientation from the nitrogen end to the carbon end, and
wherein the second and rightmost vertical line segment represents a hydrogen site, or wherein the second and rightmost vertical line segment represents a carbon site.
- nitrogen bond and a vertical line segment attached on each side of the horizontal line segment, the first and leftmost vertical line segment representing an oxygen site, wherein the relative position of the first and leftmost vertical line segment corresponds to the location of the oxygen atom on the backbone of the peptide unit when traversed in its natural orientation from the nitrogen end to the carbon end, and
Specification