Abstract: Embodiments of the present disclosure generally relate to the field of electronic data communications, and more specifically to transport methods for hierarchical data networks in relation to providing “address-less data transport” of data packets. An order is introduced or associated with nodes to establish relationships, and the order may be stored in the form of a tree topology in a data structure. The order of nodes is thus known, and logic and/or other data sets, data payloads, etc., may be transmitted across the nodes, wherein the steps to execute the transmission are more efficient due to the properties of the ordered nodes. Each node in the plurality of nodes is comprised of a plurality of network interfaces, which through pairwise joining, forms a data network of a tree topology.

Abstract: The invention provides a computer implemented method of quantifying the quality of packing for a residue comprising one or more residue atoms in a first protein in a first conformation, the method comprising: (a) calculating one or more close contact potentials based on a distance between the one or more residue atoms and one or more environment atoms, (b) calculating a contact area of the one or more residue atoms that is exposed to the one or more environment atoms and (c) calculating a close contact surface density (CCSD) by dividing the sum of the one or more close contact potentials by the contact area.

Abstract: Systems and methods for visualization of a molecule, comprising a set of particles, are provided. A set of three-dimensional coordinates is obtained, each coordinate describing a position for a corresponding particle. A cost function containing an error in a set of two-dimensional coordinates, where each two-dimensional coordinate corresponds to a three-dimensional coordinate in the set of three-dimensional coordinates, is minimized until an exit condition is achieved. The minimization alters the two-dimensional coordinate values. A set of physical properties SM is obtained, each such property representing a property shared by a pair of particles in the molecule. The coordinates are plotted as nodes of a two-dimensional graph after minimization, connected by a plurality of edges. An edge connects a coordinate pair in the graph that corresponds to a pair of particles in the molecule. A characteristic of the edge is determined by a physical property for the pair of particles.

Abstract: Systems and methods for variable fitting include communicating one or more descriptions for a system exhibiting a variable value. In response, a response consisting of a first or second indication is received from the user of the disclosed systems and methods. The first and second indications being that the one or more descriptions are respectively considered to be in a first or second class with respect to the variable. The variable value is changed based on the received response. This communicating, receiving, and changing is repeated until an exit condition is considered to exist.

Abstract: Systems and methods for visualization of a molecule, comprising a set of particles, are provided. A set of three-dimensional coordinates is obtained, each coordinate describing a position for a corresponding particle. A cost function containing an error in a set of two-dimensional coordinates, where each two-dimensional coordinate corresponds to a three-dimensional coordinate in the set of three-dimensional coordinates, is minimized until an exit condition is achieved. The minimization alters the two-dimensional coordinate values. A set of physical properties SM is obtained, each such property representing a property shared by a pair of particles in the molecule. The coordinates are plotted as nodes of a two-dimensional graph after minimization, connected by a plurality of edges. An edge connects a coordinate pair in the graph that corresponds to a pair of particles in the molecule. A characteristic of the edge is determined by a physical property for the pair of particles.

Abstract: The invention provides a method of determining changes in a first set of residues r1 due to changes in a second set of residues r2 in a protein system comprising one or more proteins comprising r1 and r2. In exemplary embodiments, the method comprises optimizing a quality function Q by modifying one or more properties of r1 and r2 in a constrained environment in which all degrees of freedom of the system except those directly involved in the potential coupling between r1 and r2 are removed.

Abstract: Systems and methods for two-dimensional visualization of a molecule, comprising the set of particles {p1, . . . , pN}, are provided. A set of N three-dimensional coordinates {x1, . . . , xN} is obtained, each xi in {x1, . . . , xN} describing a three-dimensional position for a corresponding particle pi in {p1, . . . , pN}. A cost function containing the error in a set of two-dimensional coordinates (c1, . . . , cN), where each ci in (c1, . . . , cN) corresponds to a three-dimensional coordinate xi in {x1, . . . , xN}, is minimized until an exit condition is achieved. The minimization alters the values of (c1, . . . , cN). A set of physical properties SM is obtained, each si,j in SM representing a physical property shared by a pair of particles (pi, pj) in {p1, . . . , pN}. Coordinates (c1, . . . , cN) are plotted as nodes of a two-dimensional graph after minimization. A plurality of edges for the graph is plotted.

Abstract: Provided is a method of quantitatively determining the ability of individual IgG heavy chains to selectively pair with a particular IgG light chain when the heavy chains and two unique light chains are co-expressed. The method provides results with reasonable throughput and is robust and accurate. The co-expressed heavy and light chains do not need to be isolated and purified which enables more efficient screening.

Abstract: Systems and methods for physical parameter fitting include communicating one or more three-dimensional structures for a molecular system exhibiting a physical parameter value. In response, a dichotomous classification consisting of a first or second indication is received from the user of the disclosed systems and methods. The first and second indications being that the one or more three-dimensional structures are respectively deemed to be in a first or second dichotomous structural class with respect to the physical parameter. The physical parameter value is altered based on the received dichotomous classification. This communicating, receiving, and altering is repeated until an exit condition is deemed to exist.

Abstract: Systems and methods for two-dimensional visualization of a molecule, comprising the set of particles {p1, . . . , pN}, are provided. A set of N three-dimensional coordinates {x1, . . . , xN} is obtained, each xi in {x1, . . . , xN} describing a three-dimensional position for a corresponding particle pi in {p1, . . . , pN}. A cost function containing the error in a set of two-dimensional coordinates (c1, . . . , cN), where each ci in (c1, . . . , cN) corresponds to a three-dimensional coordinate xi in {x1, . . . , xN}, is minimized until an exit condition is achieved. The minimization alters the values of (c1, . . . , cN). A set of physical properties SM is obtained, each si,j in SM representing a physical property shared by a pair of particles (pi, pj) in {p1, . . . , pN}. Coordinates (c1, . . . , cN) are plotted as nodes of a two-dimensional graph after minimization. A plurality of edges for the graph is plotted.

Abstract: Rationally designed antibodies and polypeptides that comprise multiple Fc region amino acid substitutions that synergistically provide enhanced selectivity and binding affinity to a target Fc receptor are provided. The polypeptides are mutated at multiple positions to make them more effective when incorporated in antibody therapeutics than those having wild-type Fc components.

Abstract: Rationally designed antibodies and polypeptides that comprise multiple Fc region amino acid substitutions that synergistically provide enhanced selectivity and binding affinity to a target Fc receptor are provided. The polypeptides are mutated at multiple positions to make them more effective when incorporated in antibody therapeutics than those having wild-type Fc components.

Abstract: Provided is a method of quantitatively determining the ability of individual IgG heavy chains to selectively pair with a particular IgG light chain when the heavy chains and two unique light chains are co-expressed. The method provides results with reasonable throughput and is robust and accurate. The co-expressed heavy and light chains do not need to be isolated and purified which enables more efficient screening.

Abstract: Systems and methods for two-dimensional visualization of a molecule, comprising the set of particles {p1, . . . , pN}, are provided. A set of N three-dimensional coordinates {x1, . . . , xN} is obtained, each xi in {x1, . . . , xN} describing a three-dimensional position for a corresponding particle pi in {p1, . . . , pN}. A cost function containing the error in a set of two-dimensional coordinates (c1, . . . , cN), where each Ci in (c1, . . . , cN) corresponds to a three-dimensional coordinate xi in {x1, . . . , xN}, is minimized until an exit condition is achieved. The minimization alters the values of (c1, . . . , cN). A set of physical properties SM is obtained, each Si,j in SM representing a physical property shared by a pair of particles (pi, pj) in {p1, . . . , pN}. Coordinates (c1, . . . , cN) are plotted as nodes of a two-dimensional graph after minimization. A plurality of edges for the graph is plotted.

Abstract: The invention provides a method of determining changes in a first set of residues r1 due to changes in a second set of residues r2 in a protein system comprising one or more proteins comprising n and r2. In exemplary embodiments, the method comprises optimizing a quality function Q by modifying one or more properties of r1 and r2 in a constrained environment in which all degrees of freedom of the system except those directly involved in the potential coupling between r1 and r2 are removed.

Abstract: The invention provides a computer implemented method of quantifying the quality of packing for a residue comprising one or more residue atoms in a first protein in a first conformation, the method comprising: (a) calculating one or more close contact potentials based on a distance between the one or more residue atoms and one or more environment atoms, (b) calculating a contact area of the one or more residue atoms that is exposed to the one or more environment atoms and (c) calculating a close contact surface density (CCSD) by dividing the sum of the one or more close contact potentials by the contact area.

Abstract: Rationally designed antibodies and polypeptides that comprise two Fc region amino acid substitutions that synergistically provide enhanced selectivity and binding affinity to a target Fc receptor are provided. The polypeptides comprise Fc region mutations at two positions that synergistically make the polypeptides more effective when incorporated in antibody therapeutics than those having wild-type Fc components.

Abstract: Rationally designed antibodies and polypeptides that comprise multiple Fc region amino acid substitutions that synergistically provide enhanced selectivity and binding affinity to a target Fc receptor are provided. The polypeptides are mutated at multiple positions to make them more effective when incorporated in antibody therapeutics than those having wild-type Fc components.

Abstract: The invention provides a method of sampling conformation space for an interacting pair comprising (a) an approaching body characterized by an approaching body quaternion and (b) a central body characterized by a central body quaternion, wherein the interacting pair is characterized by an energy and a center of mass vector, the method comprising: (i) performing a first minimization of the energy by varying the approaching body quaternion through off-lattice transformations and then, sequentially, (ii) performing a first translation of the approaching body toward the central body along the center of mass vector, wherein the translation consists of an on-lattice transformation.