Molecular modelling refers to the combination of theoretical methods and computational techniques to model or mimic the behaviour of molecules. This method helps the humans to investigate the molecular modelling of biological activities like protein folding, enzyme catalysis, protein stability and molecular recognition of proteins, DNA, and membrane complexes.
Some of the methods which are patented in USPTO are given below.
Patent no: 6,029,114 titled ‘Molecular modelling of neurotrophin-receptor binding’ with the abstract : The present invention relates to computational methods for identifying the bioactive conformations of peptide domains, in particular the geometries of complexes of neurotrophins and neurotrophin receptors, and the geometries of neurotrophin receptors and ligands. The invention includes a method for identifying and theoretically modelling a receptor binding site for neurotrophins, such as NGF, BDNF, NT-3 and NT4/5, of the common neurotrophin receptor p75.sup.NTR. The principal residues of the p75.sup.NTR binding site are Asp.sup.47p, Lys.sup.56p, Asp.sup.75p, Asp.sup.76p, Asp.sup.88p and Glu.sup.88p of the second and third cysteine-rich domains. These residues interact with residues of variable loop regions I and V and other neighboring residues of each of the neurotrophins. The invention provides a method of designing a ligand for binding with common neurotrophin receptor p75.sup.NTR including computationally evolving a ligand having effective moieties located relative to each other in the ligand so that the moieties bind to at least two of p75.sup.NTR binding loop 2A including region Cys.sup.39p to Cys.sup.58p, p75.sup.NTR binding loop 2B including region Cys.sup.58p to Cys.sup.78p, and p75.sup.NTR binding loop 3A including region Cys.sup.79p to Cys.sup.94p. The invention further provides a method of identifying such a ligand encoded in a data base containing molecules coded for spatial occupancy, relative atomic position, bond type and/or charge. The designed or identified ligand may be an agonist or antagonist of p75.sup.NTR.
Patent no: 6,291,247 titled ‘Methods of screening for factors that disrupt neurotrophin conformation and reduce neurotrophin biological activity’ with the abstract: Factors and methods for disrupting or inhibiting the association of protomers of a multimeric protein are described. Such inhibition reduces the biological disorders. Particularly, novel neurotrophin antagonists are described. Generally, the antagonist comprises amino acids from positions 68-58 and 108-110 of a neurotrophin, in which the amino acid from position 68 is covalently bound to the amino acid from position 108 and the amino acid from position 58 is covalently bound to the amino acid at position 110 to form a bicyclic structure, in another aspect of the invention transition metal ions are provided for selectively altering the geometry of the receptor binding domains of neurotrophins which allows functionality and activity of the neurotrophins to be selectively reduced. For example Zn.sup.2+ alters the conformation of NGF rendering it unable to bind to p75.sup.NTR or TrkA receptors or to activate signal transduction and biological outcomes normally induced by this protein. Molecular modelling studies predict that Zn.sup.2+ binding to NGF will induce structural changes within domains of this neurotrophin which participate in the recognition of TrkA and p75.sup.NTR. Ni.sup.2+ on the other hand selectively alters the conformation of NGF rendering it unable to bind to TrkA but does not affect binding to p75.sup.NTR. Similar actions of Zn.sup.2+ are also observed with other members of the NGF family, suggesting a modulatory role for the metal ions in neurotrophin function.Patent no : titled with the abstract :
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