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US 6,389,378 B2Granted
Method of searching novel ligand compounds from three-dimensional structure database
OwnerAkiko Itai, Miho Mizutaniinventors
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OwnerAkiko Itai, Miho Mizutaniinventors
Estimating the term…
A method of searching one or more ligand-candidate compounds to a target biopolymer from a three-dimensional structure database, which comprises the steps of: (i) the first step of assigning hydrogen-bonding category numbers, information for calculating force-field energy, and information for generating conformations to two or more trial compounds in addition to atomic three-dimensional coordinates thereof; (ii) the second step of preparing physicochemical information about a ligand-binding region and one or more dummy atoms based on the three-dimensional atomic coordinates of the target biopolymer;(iii) the third step of estimating the most stable docking structure, wherein said step further comprises the steps of examining possible docking structures by docking a trial compound to the biopolymer while varying conformations of the trial compound, evaluating interaction energies between the target biopolymer and the trial compound, and repeating structure optimization; (iv) the fourth step of deciding whether or not the trial compound should be adopted as a ligand-candidate compound based on given criteria including the interaction energy values between the target biopolymer and the trial compound in the most stable docking structure estimated according to the step (iii); and (v) the fifth step of repeating the step (iii) and the step (iv) for all of the trial compounds.
A method of selecting at least one ligand-candidate compound suitable for binding to a target biopolymer, from a compound database comprising information of three-dimensional coordinates of at least two database entries in arbitrary conformation comprising:
A compound database stored on a computer readable medium for searching at least one ligand-candidate compound for a biopolymer, the database comprising three-dimensional coordinates of at least two database entries, atomic coordinates of hydrogen atoms, force field atom-type, atomic charge of atoms, hydrogen bonding category number of heteroatoms, rotatable bonds, and bond rotation schemes for the rotatable bonds, wherein the database is searchable to find at least one ligand-candidate compound.
A method of selecting at least one ligand-candidate compound suitable for binding to a target biopolymer from a compound database comprising information of three-dimensional coordinates of at least two database entries in arbitrary conformation comprising:
A method of selecting at least one ligand-candidate compound suitable for binding to a target biopolymer from a compound database comprising information of three-dimensional coordinates of at least two database entries in arbitrary conformation estimating the most stable docking structure between the target biopolymer and each of at least two entries as a trial compound wherein the estimating comprises consideration of the possible binding modes and conformations of the trial compound.
A method of selecting at least one ligand-candidate compound suitable for binding to a target biopolymer from a compound database comprising estimating the most stable docking structure between the target biopolymer and each of at least two entries as a trial compound by an automatic docking method;
A method of selecting at least one ligand-candidate compound suitable for binding to a target biopolymer from a compound database comprising estimating the most stable docking structure between the target biopolymer and each of at least two entries as a trial compound by an automatic docking method;
A method of selecting at least one ligand-candidate compound suitable for binding to a target biopolymer from a compound database comprising estimating the most stable docking structure between the target biopolymer and each of at least two entries as a trial compound;
A compound database stored on a computer readable medium for searching at least one ligand-candidate compound for a biopolymer comprising information for calculating interaction energy and information for generating conformations.
Dependencies are inferred from the claim text.