Methods, apparatus and computer program products for formulating culture media
First Claim
1. A method of identifying a culture medium component, comprising the steps of:
- measuring first indicia of a property of a plurality of first culture media which each contains a respective first test compound from within a first test library, determining a relationship between at least one parameter of the first test compounds and the measured first indicia of the property of the plurality of first culture media;
determining a test requirement relating to the measured first indicia; and
identifying a second test library containing a plurality of second test compounds as components of a plurality of second culture media which based on the relationship are expected to provide second indicia of the property which meets the test requirement.
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Abstract
Methods, apparatus and computer program products are provided for identifying a component of culture medium based on the parameters (e g, physical, chemical, biological and/or topological characteristics) of compounds from within a compound library. In preferred embodiments, the compound library is a peptide library. Also provided are methods of selecting a compound library from a larger compound space based on whole molecule (i.e., global) parameters of the compounds. Preferably, this method is practiced in conjunction with a method of identifying a component of a culture medium. Further provided are methods of predicting a biological activity of a peptide based on at least one whole molecule parameter of the peptide. This method finds use in methods of drug discovery, identifying components of culture medium, and identifying and/or designing peptides with particular pharmacological or therapeutic activities.
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Citations
127 Claims
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1. A method of identifying a culture medium component, comprising the steps of:
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measuring first indicia of a property of a plurality of first culture media which each contains a respective first test compound from within a first test library, determining a relationship between at least one parameter of the first test compounds and the measured first indicia of the property of the plurality of first culture media;
determining a test requirement relating to the measured first indicia; and
identifying a second test library containing a plurality of second test compounds as components of a plurality of second culture media which based on the relationship are expected to provide second indicia of the property which meets the test requirement. - 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, 27, 28, 29, 30)
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- 31. A method of defining a test compound library, comprising the step of representing each of a plurality of groups of compound isomers from within a compound space as a respective candidate compound.
- 36. A test compound library wherein each of a plurality of compound isomers from within a compound space is represented as a respective candidate compound.
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41. A method of Identifying a culture medium component, comprising the steps of:
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defining a first test library by representing each of a plurality of groups of compound isomers from within a compound space as a respective candidate compound;
measuring first indicia of a property of a plurality of first culture media which each contains a respective first test compound from within the first test library;
determining a relationship between at least one parameter of the first test compounds and the measured first indicia of the property of the plurality of first culture media;
determining a test requirement relating to the measured first indicia; and
identifying a plurality of second test compounds from within the compound space as components of a plurality of second culture media which based on the relationship are expected to provide second indicia of the property which meets the test requirement. - View Dependent Claims (42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58)
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59. A method of predicting indicia of a property of a peptide, comprising the steps of:
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measuring indicia of an activity of a plurality of test peptides from a test peptide library;
determining a relationship between the measured indicia of the activity and at least one whole molecule parameter of the plurality of test peptides;
predicting the indicia of the activity of a peptide not within the plurality of test peptides based on the relationship. - View Dependent Claims (60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73)
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74. A method of identifying a peptide with a predicted indicia of an activity that satisfies a test requirement, comprising the steps of:
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measuring first indicia of an activity of a plurality of first test peptides from a first test peptide library;
determining a relationship between the measured first indicia of the activity and at least one whole molecule parameter of the plurality of first test peptides;
determining a test requirement relating to the measured first indicia; and
identifying a second test peptide library containing a plurality of second test peptides which based on the relationship are expected to provide second indicia of the activity that meets the test requirement. - View Dependent Claims (75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95)
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96. A method of identifying a culture medium component, comprising the steps of:
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culturing a plurality of first cell cultures in a plurality of first culture media each containing a respective first test compound from a first test library;
measuring first indicia of a property of the plurality of first culture media in the plurality of first cell cultures;
determining a relationship between the measured first indicia of the property and at least one parameter of the plurality of first culture media;
determining a test requirement relating to the measured first indicia; and
culturing a plurality of second cell cultures in a plurality of second culture media each containing a respective second test compound from a second test library;
wherein based on the relationship the plurality of second culture media containing the second test compounds are predicted to give indicia of the property that satisfy the test requirement. - View Dependent Claims (97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 127)
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119. An apparatus for identifying a culture medium component, comprising:
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means for determining a relationship between measured first indicia of a property of a plurality of first culture media which each contains a respective first test compound from within a first test library and at least one parameter of the first test compounds; and
means for identifying a second test library containing a plurality of second test compounds as components of a plurality of second culture media which based on the relationship are expected to provide second indicia of the property which meets a test requirement relating to the measured first indicia. - View Dependent Claims (120, 121, 122)
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123. A computer program product readable by a machine and tangibly embodying a program of instructions executable by the machine to perform the method steps of:
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determining a relationship between measured first indicia of a property of a plurality of first culture media which each contains a respective first test compound from within a first test library and at least one parameter of the first test compounds; and
identifying a second test library containing a plurality of second test compounds as components of a plurality of second culture media which based on the relationship are expected to provide second indicia of the property which meets a test requirement relating to the measured first indicia. - View Dependent Claims (124, 125, 126)
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Specification