Abstract: Systems and methods for building a comprehensive genome scale metabolic model. The method includes determining that at least one of a hypothetical profile annotation and an uncharacterized profile annotation is available in a profile annotation associated with a protein. Further, the method includes performing a machine learning procedure on at least one of the hypothetical profile annotation and the uncharacterized hypothetical profile annotation after a fuzzy string matching and ranking procedure. Further, the method includes obtaining all the possible protein annotations based on a fuzzy string matching procedure. Further, the method includes performing a rank procedure on at least one of the hypothetical profile annotation and the uncharacterized profile alternative annotation. Further, the method includes identifying all possible metabolic reactions for the protein annotation obtained by the fuzzy string matching procedure.

Abstract: Provided are a method and device for assessing a feasibility of one or more biochemical reactions in an organism. The method includes receiving an input representing the organism and input representing one or more biochemical reactions that are to be assessed; computing a reaction feasibility score for each of the one or more input biochemical reactions a knowledgebase; and selecting the biochemical reaction that is likely to occur in the organism.

Abstract: Embodiments herein disclose a method for identifying co-evolving sites and and at least one substituent amino acid residue. The method includes obtaining a current state of a protein and an ancestral state of the protein. Further, the method includes determining at least one amino acid substitution along with at least one co-evolving site associated with the protein based on the current state of the protein and the ancestral state of the protein. Further, the method includes assessing the at least one amino acid substitution as a function of a nucleotide substitution in the protein. Further, the method includes assessing at least one co-evolving site substitution based on the at least one assessed amino acid substitution. Further, the method includes identifying the co-evolving sites and at least one substituent amino acid residue.

Abstract: Systems and methods for building a comprehensive genome scale metabolic model. The method includes determining that at least one of a hypothetical profile annotation and an uncharacterized profile annotation is available in a profile annotation associated with a protein. Further, the method includes performing a machine learning procedure on at least one of the hypothetical profile annotation and the uncharacterized hypothetical profile annotation after a fuzzy string matching and ranking procedure. Further, the method includes obtaining all the possible protein annotations based on a fuzzy string matching procedure. Further, the method includes performing a rank procedure on at least one of the hypothetical profile annotation and the uncharacterized profile alternative annotation. Further, the method includes identifying all possible metabolic reactions for the protein annotation obtained by the fuzzy string matching procedure.

Abstract: Accordingly, embodiments herein disclose a method for handling an enzyme function through at least one change at multiple sites in an enzyme. The method includes detecting, by an electronic device, one or more functionally linked site pairs from the multiple sites in the enzyme. Further, the method includes determining, by the electronic device, at least one criticality assessment function for the one or more functionally linked site pairs. Further, the method includes prioritizing, by the electronic device, the functionally linked site pairs based on at least one of the criticality assessment function, a functional linkage strength, and a spatial linkage metric. Further, the method includes identifying, by the electronic device, the multiple sites from the prioritized functionally linked site pairs as optimum sites for introducing a change to handle the enzyme function.

Abstract: An apparatus and methods for assessing an ability of an organism(s) to metabolize toxic compounds, in a computing environment. Embodiments herein relates to the field of metabolic engineering in biochemical pathways and more particularly to an apparatus and methods for assessing an ability of an organism, a strain of the organism or strain of a different organism(s), to metabolize toxic compounds. The method includes receiving an input corresponding to at least one of a metabolite/compound data, at least one reaction data and at least one pathway data. The received input may be assessed to identify toxic compound(s). Further, reactions and pathway(s) may be determined in the identified toxic compound(s). Furthermore, the identified reactions and pathway(s) may be classified as potential toxic generating route(s) or toxic degrading route(s). The assessment can be used for performing comparative assessment of different strains of an organism/different organisms to achieve reaction diversity.

Abstract: Provided are a method and a device for selecting a pathway for a target compound by combining biochemical and chemical processes together, wherein an input of at least one pathway for synthesis of a target compound or degradation into a target compound is received, hybrid arrangements of one or more reaction steps included in the at least one pathway are predicted, a pathway feasibility score is computed, and at least one hybrid arrangement is selected based on the pathway feasibility score.

Abstract: A method of predicting an amino acid substitution includes: receiving input of information regarding a structure of an enzyme along with the site of the enzyme in proximity to a bound ligand; identifying a functional atom of a wild type (WT) amino acid at the site of interest and a functional atom of the ligand; confirming properties of the functional atom of the WT amino acid and the functional atom of the ligand; detecting whether an interaction exists between the functional atom of the WT amino acid and the functional atom of the ligand; selecting alternative amino acids according to a result of the detecting of the interaction; determining a score for each of the selected alternative amino acids, respectively; ranking the selected alternative amino acids, based on the scores; and predicting substitutions of alternative amino acids having high rankings from among the selected alternative amino acids.

Abstract: Provided is a recombinant microorganism including an exogenous gene encoding a bacterial cytochrome P450 protein or a variant thereof, a composition including the recombinant P450 protein or the variant thereof, which is used for removing CHnF4-n (n is an integer of 0 to 3) in a sample, and a method of reducing a concentration of CHnF4-n in the sample.

Abstract: Methods and devices for selecting and optimizing an enzyme that catalyzes an input reaction. Known methods for in-silico selection and engineering of an enzyme are computationally intensive and have faulty accuracy. However, the present methods and devices rapidly and accurately screen multiple enzymes and optimize the same for an input reaction by performing stages including enzyme selection, enzyme assessment, and enzyme position scoring. Significant enhancement of the efficacy of the enzyme in a chemical reaction may be achieved through enzyme optimization.

Abstract: Provided are a method and device for assessing a feasibility of one or more biochemical reactions in an organism. The method includes receiving an input representing the organism and input representing one or more biochemical reactions that are to be assessed; computing a reaction feasibility score for each of the one or more input biochemical reactions a knowledgebase; and selecting the biochemical reaction that is likely to occur in the organism.

Abstract: Provided are a recombinant microorganism including an exogenous gene encoding a soluble methane monooxygenase protein, a composition including the soluble methane monooxygenase, which is used for removing CHnF4-n (n is an integer of 0 to 3) in a sample, and a method of reducing a concentration of CHnF4-n in the sample.

Abstract: Provided is a recombinant microorganism including an exogenous gene encoding a bacterial cytochrome P450 protein or a variant thereof, a composition including the recombinant P450 protein or the variant thereof, which is used for removing CHnF4-n (n is an integer of 0 to 3) in a sample, and a method of reducing a concentration of CHnF4-n in the sample.