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1. (WO2012120438) SYSTEMS AND METHODS FOR USE IN MOLECULAR DRUG DESIGN
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CLAIMS:

1 . A method for molecular drug design, the method comprising:

selecting a ligand from a ligand database;

screening physico-chemical properties of the selected ligand against physico- chemical properties of entries comprising a sequence database, said sequence database entries comprising physico-chemical properties of at least one nucleic acid, RNA, DNA, protein or amino acid sequence, to ascertain at least one physico-chemically favourable interaction between the selected ligand and a sequence; and

displaying the at least one physico-chemically favourable interaction as an output.

2. A method for molecular drug design, the method comprising:

selecting a nucleic acid, RNA, DNA, protein or amino acid sequence from a sequence database comprising at least one nucleic acid, RNA, DNA, protein or amino acid sequence;

screening physico-chemical properties of the sequence against physico-chemical properties of entries comprising a ligand database, said ligand database entries comprising physico-chemical properties of at least one ligand, to ascertain at least one physico-chemically favourable interaction between the selected sequence and a ligand; and

displaying the at least one physico-chemically favourable interaction as an output.

3. The method of claim 1 or 2, further comprising the step of selecting a disorder/disease from a disorder/disease database therein customizing the sequence database and the ligand database to comprise at least one nucleic acid, RNA, DNA, protein or amino acid sequence and ligand associated with the selected disorder/disease such that the screening is limited to ligands and sequences associated with the selected disease.

4. The method of any one of claims 1 to 3, further comprising the step of selecting a binding class and/or mode from a binding class and/or modes database such that the screening is limited to ascertaining at least one physico-chemically favourable interaction of the selected binding mode.

5. The method of claim 4, wherein the binding classes include at least one of the following group: intercalation, modification, addition and cavity fitting, and wherein the binding modes include at least one of the following group: alkylation, mono-alkylation, bis- alkylation, cycloaddition, adduct, bulge fit and triplex binding.

6. The method of any one of claims 1 to 5, wherein the at least one physico-chemically favourable interaction is shown in the output as a two or three dimensional graphical representation showing how the ligand and sequence interact with each other.

7. The method of any one of claims 1 to 6, wherein the displayed at least one physico- chemically favourable interaction comprises a description of the interaction including of at least one of the group occurring as a result of the favourable interaction: bond types, bond lengths, bond strengths, classes of binding, modes of binding and types of atomic interactions.

8. The method of any one of claims 1 to 7, wherein the displayed at least one physico- chemically favourable interaction comprises at least one annotation which annotation highlights a region of the sequence and/or of the ligand where the favourable interaction occurs.

9. The method of any one of claims 1 to 8, wherein the ligand is a drug molecule.

10. The method of any one of claims 1 to 9, wherein the screening takes place via at least one of the following methods: comparing empirical data, molecular force field techniques, quantum mechanical techniques and/or hybrids of the aforementioned.

1 1 . A system for use in molecular drug design, the system comprising:

a sequence database containing physico-chemical properties of at least one nucleic acid, RNA, DNA, protein or amino acid sequence; and

a ligand database containing physico-chemical properties of at least one ligand; and

a processor arranged to allow a user to select a ligand from the ligand database, the selected ligand is screened against entries of the sequence database to ascertain at least one physico-chemically favourable interaction between the selected ligand and an entry of the sequence database, said at least one physico-chemicallly favourable interaction being displayed by the processor as an output.

12. A system for use in molecular drug design, the system comprising:

a sequence database containing physico-chemical properties of at least one nucleic acid, RNA, DNA, protein or amino acid sequence;

a ligand database containing physico-chemical properties of at least one ligand; and

a processor arranged to allow a user to select a nucleic acid, RNA, DNA, protein or amino acid sequence from a sequence database comprising at least one nucleic acid, RNA, DNA, protein or amino acid sequence, the selected nucleic acid, RNA, DNA, protein or amino acid sequence is screened against entries of the ligand database to ascertain at least one physico-chemically favourable interaction between the selected nucleic acid, RNA, DNA, protein or amino acid sequence and an entry of the ligand database, said at least one physico-chemicallly favourable interaction being displayed by the processor as an output.

13. The system of claim 1 1 or 12, further comprising a disorder/disease database containing a list of disorders/diseases, the processor further arranged to allow the user to select a disorder/disease from the disorder/disease database so as to customize the sequence database and the ligand database to comprise at least one nucleic acid, RNA, DNA, protein or amino acid sequence and ligand associated with the selected disorder/disease such that the screening is limited to ligands and sequences associated with the selected disease.

14. The system of any one of claims 1 1 to 13, further comprising a binding class and/or modes database containing a list of binding classes and/or modes, the processor further arranged to allow the user to select a binding class and/or mode from the binding classes and/or modes database such that the screening is limited to ascertaining at least one physico-chemically favourable interaction of the selected binding class and/or mode.

15. The system of claim 14, wherein the binding classes include at least one of the following group: intercalation, modification, addition and cavity fitting, and wherein the binding modes include at least one of the following group: alkylation, mono-alkylation, bis- alkylation, cycloaddition, adduct, bulge fit and triplex binding.

16. The system of any one of claims 1 1 to 15, wherein the displayed at least one physico- chemically favourable interaction is shown in the output as a two or three dimensional graphical representation showing how the ligand and sequence interact with each other.

17. The system of any one of claims 1 1 to 16, wherein the at least one physico-chemically favourable interaction comprises a description of the interaction including of at least one of the group occurring as a result of the favourable interaction: bond types, bond lengths, bond strengths, classes of binding, modes of binding and types of atomic interactions..

18. The system of any one of claims 1 1 to 17, wherein the at least one physico-chemically favourable interaction comprises at least one annotation which annotation highlights a region of the sequence and/or of the ligand where the favourable interaction occurs.

19. The system of any one of claims 1 1 to 28, wherein the ligand is a drug molecule.

20. The system of any one of claims 1 1 to 19, wherein the screening takes place via at least one of the following methods: comparing empirical data, molecular force field techniques, quantum mechanical techniques and/or hybrids of the aforementioned.