-
公开(公告)号：US20220148685A1
公开(公告)日：2022-05-12
申请号：US17092910
申请日：2020-11-09
Applicant: X Development LLC
Inventor： Frank Russo
Abstract: Embodiments include simulating the behavior of enzymatic reactions involving multiple substrates binding with an enzyme. Some embodiments may allow for modeling the reactions without requiring known values for kinetic rate constants for microsteps of the reaction. Embodiments may include computer-implemented methods. Methods may include initializing an initial free energy profile for a reaction. The initial free energy profile may include a plurality of initial waypoints. The methods may include generating a plurality of rate equations, each rate equation representing a component step of the plurality of component steps. Methods may include simulating an in silico behavior of the reaction. Simulating may include generating concentrations of the substrates using the plurality of rate equations. Simulating may include updating the plurality of initial waypoints to reduce a difference between the in silico behavior of the reaction and an expected behavior of the reaction, forming a new free energy profile comprising a plurality of updated waypoints.
-
公开(公告)号：US20220148684A1
公开(公告)日：2022-05-12
申请号：US17093057
申请日：2020-11-09
Applicant: X Development LLC
Inventor： Frank Russo
IPC: G16C20/10
Abstract: Embodiments include simulating the behavior of enzymatic reactions in silico in place of or in addition to running in vitro experiments. The in silico simulations may involve varying the initial concentrations of the reactant while setting the rate of change of concentration each form of an enzyme to be at steady state, which may aid in realistically representing the kinetics of the reaction. Some embodiments may allow for modeling enzymatic reactions so as to obtain mathematical relationships between the reaction rate and initial concentration of a reactant. Some embodiments may determine rate constants for microscopic steps within the enzymatic reactions. In addition, some embodiments may include optimizing for a plurality of initial reactant concentrations simultaneously rather than optimizing for one initial reactant concentration at a time, in order to generate a velocity versus concentration curve and to determine the catalytic rate constant kcat and Michaelis constant Km.
-
公开(公告)号：US20190228130A1
公开(公告)日：2019-07-25
申请号：US15876962
申请日：2018-01-22
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
Abstract: A method for analyzing a bipartite graph data structure to condense reaction pathways of a metabolic network is described herein. A cell's metabolic network is structured as a bipartite graph, with molecule nodes representing the molecules within metabolism and edges connecting molecule nodes representing chemical reactions or processes. Molecule nodes within the bipartite graph are categorized according to the number of edges leading into and out of each node. If the structure of the bipartite graph indicates that the molecule node does not contribute to flux value solutions of a mathematical model of the metabolic network, then the node and its connected reaction pathway is blocked or removed from the bipartite graph. Thus the complexity of the bipartite graph may be reduced, and crucial nodes and pathways identified.
-
公开(公告)号：US20220036975A1
公开(公告)日：2022-02-03
申请号：US16942210
申请日：2020-07-29
Applicant: X Development LLC
Inventor： Frank Russo
Abstract: The present disclosure relates to general and scalable techniques for modeling in silico the kinetics of systems of connected biochemical reactions. Particularly, aspects of the present disclosure are directed to deconstructing a reaction into a plurality of component steps, translating each component step into a set of rate equations to obtain a standard mathematical construct or model representing each component step, numerically integrating across the standard mathematical constructs or models using a system of ordinary differential equations to determine a contribution of each component step to a rate of change of molecules within reaction, and deriving a in silico behavior of a system utilizing the reaction based on the contribution of each component step to the rate of change of the molecules within the reaction. The standard mathematical constructs or models may be parameterized based on an energy profile for the reaction inferred from machine-learning approaches.
-
公开(公告)号：US11183273B2
公开(公告)日：2021-11-23
申请号：US15694500
申请日：2017-09-01
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
Abstract: A method for simulating a biochemical environment utilizes a heterogeneous process model, which evaluates both a flux balance analysis and one or more detailed models each on a different but overlapping sets of molecules in the biochemical environment. The heterogeneous process model evaluates the flux balance analysis based on a stoichiometric matrix, a flux vector including initial internal exchange flux values, and an objective function. The heterogeneous process model evaluates the one or more detailed models based on an initial set of molecule concentrations and a plurality of detailed model parameters. The results are then used to update the exchange fluxes and molecules concentrations. The process is repeated thereby integrating the results of the flux balance analysis with the one or more detailed models.
-
Patent Agency Ranking
公开(公告)号：US20190073433A1
公开(公告)日：2019-03-07
申请号：US15694506
申请日：2017-09-01
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
Abstract: A bipartite graph structure is utilized to better store data. The bipartite graph structure may be used in a biochemical database to efficiently store a variety of molecules and processes that might occur between the molecules. Molecules are represented as molecule nodes, which may have metadata fields including a molecule name, a molecule type, a molecular formula, a sequence, a molecular charge, a set of molecular properties, and a set of component molecules. Processes operating on the molecules are represented by process nodes, which may have metadata fields including a process name, a set of process roles, a set of process properties, and a set of sub-processes. Edges, called roles, each associate a molecule node with a process node and represent the role the associated molecule plays in the associated process. The roles may contain metadata identifying the role type and the stoichiometry coefficient of the molecule in the process.
-
公开(公告)号：US11024403B2
公开(公告)日：2021-06-01
申请号：US15876962
申请日：2018-01-22
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
IPC: G01N33/48 , G01N33/50 , G16B5/00 , G16C20/10 , G06F16/332 , G06F16/901
Abstract: A method for analyzing a bipartite graph data structure to condense reaction pathways of a metabolic network is described herein. A cell's metabolic network is structured as a bipartite graph, with molecule nodes representing the molecules within metabolism and edges connecting molecule nodes representing chemical reactions or processes. Molecule nodes within the bipartite graph are categorized according to the number of edges leading into and out of each node. If the structure of the bipartite graph indicates that the molecule node does not contribute to flux value solutions of a mathematical model of the metabolic network, then the node and its connected reaction pathway is blocked or removed from the bipartite graph. Thus the complexity of the bipartite graph may be reduced, and crucial nodes and pathways identified.
-
公开(公告)号：US10657179B2
公开(公告)日：2020-05-19
申请号：US15694506
申请日：2017-09-01
Applicant: X Development LLC
Inventor： Jason Thompson , Frank Russo
Abstract: A bipartite graph structure is utilized to better store data. The bipartite graph structure may be used in a biochemical database to efficiently store a variety of molecules and processes that might occur between the molecules. Molecules are represented as molecule nodes, which may have metadata fields including a molecule name, a molecule type, a molecular formula, a sequence, a molecular charge, a set of molecular properties, and a set of component molecules. Processes operating on the molecules are represented by process nodes, which may have metadata fields including a process name, a set of process roles, a set of process properties, and a set of sub-processes. Edges, called roles, each associate a molecule node with a process node and represent the role the associated molecule plays in the associated process. The roles may contain metadata identifying the role type and the stoichiometry coefficient of the molecule in the process.
-
9.发明授权公开(公告)号：US11776659B1
公开(公告)日：2023-10-03
申请号：US16443968
申请日：2019-06-18
Applicant: X DEVELOPMENT LLC
Inventor： Jana Hartman , Frank Russo
IPC: G16B5/30
CPC classification number: G16B5/30
Abstract: Techniques for simulating networks using dynamics-based constraints are disclosed.
-
10.发明授权公开(公告)号：US11380420B1
公开(公告)日：2022-07-05
申请号：US15973415
申请日：2018-05-07
Applicant: X Development LLC
Inventor： Frank Russo , Jason Thompson , Nicholas Casavant , Yu Tanouchi
IPC: G06F3/0484 , G16B5/00 , G06F8/41 , G06N5/02 , G16B45/00 , G06F3/04847
Abstract: A system is described for constructing a biological simulation using inputs from a knowledge base data structure and one or more templates. The knowledge base data structure comprises a set of entries representing distinct molecules and chemical reactions specific within the cell. Each template defines a sub-model program specification and a set of sub-model parameters to further characterize the sub-model specification. A graphical user interface is presented on a display for a user to view and select a templates and to assign information from the knowledge base to the selected template. From the graphical user interface, the user selects multiple templates to be included in the simulation and information from the knowledge base generally describing the cell. Based on the information selected from the graphical user interface, a compiler generates a simulation configuration data file comprising computer code capable of being executed by a simulation engine.
-
-
-
-
-
-
-
-
-
Search Results
18
records
(took 0.024 seconds)
