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5436850 Method to identify protein sequences that fold into a known three-dimensional structure
PATENT ABSTRACTS
presence of the released receptor or receptor/complex in biological samples and may be used to diagnose or monitor patients with disorders or diseases that elicit or involve T cell response who exhibit elevated serum level of the receptor or receptor/complex. In addition, the cell free T cell antigen receptors themselves may be used diagnostically and/or therapeutically for diseases or conditions that are not easily addressed using immunogiobulins.
505
environment string. These frequencies are determined from a database of known protein structures and aligned sequences. The method determines the most favorable alignment of a target protein sequence to the residue positions defined by the environment string, and determines a best fit alignment score, Sij, for the target sequence. Each target sequence may then be further characterized by a ZScore, which is the number of standard deviations that Sij for the target sequence is above the mean alignment score for other target sequences of similar length.
5436850 METHOD
TO IDENTIFY
PROTEIN SEQUENCES THAT FOLD INTO A KNOWN THREE-DIMENSIONAL STRUCTURE
5437785 APPARATUS FOR DISSOLVED GAS FLOTATION IN ANAEROBIC WASTEWATER TREATMENT
Eisenberg David; Bowie James U; Luthy Rolan Los Angeles, CA, UNITED STATES assigned to The Regents of the University of California
Roshanravan Mel Coppell, TX, UNITED STATES assigned to Darling International
A computer-assisted method for identifying protein sequences that fold into a known three-dimensional structure. The inventive method attacks the inverse protein folding problem by finding target sequences that are most compatible with profiles representing the structural environments of the residues in known three-dimensional protein structures. The method starts with a known three-dimensional protein structure and determines three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chain area that is covered by polar atoms (O,N) or water, and (3) the local secondary structure. Based on these parameters, each residue position is categorized into an environment class. In this manner, a three-dimensional protein structure is converted into a one-dimensional environment string, which represents the environment class of each residue in the folded protein structure. A 3D structure profile table is then created containing score values that represent the frequency of finding any of the 20 common amino acids structures at each position of the
An apparatus for gas entrainment of wastewater in an anaerobic wastewater treatment system, the use of which includes the steps of withdrawing wastewater from an anaerobic digester and piping it into a flotation container. Thereafter the wastewater is pumped into a flee standing tank having pressure in the tank maintained at a predetermined level through the injection into the tank of compressed gas generated by anaerobic digestion occurring in the treatment system. The wastewater is removed from the tank and pumped through a multiple jet configuration wherein gas from the tank is entrained in the wastewater as the water is injected back into the tank. The gas entrained water is then discharged from the tank back into the flotation container where the gas bubbles particles to the surface of the water to form a sludge layer. The sludge layer formed on the surface of the water in the flotation container is recycled to the digester for further increased digestion, thereby providing an efficient flotation process with increased wastewater clarification, reduced disturbance of the anaerobic bacterial sludge layer, and efficient utilization of the gas generated by anaerobic digestion in the system.
presence of the released receptor or receptor/complex in biological samples and may be used to diagnose or monitor patients with disorders or diseases that elicit or involve T cell response who exhibit elevated serum level of the receptor or receptor/complex. In addition, the cell free T cell antigen receptors themselves may be used diagnostically and/or therapeutically for diseases or conditions that are not easily addressed using immunogiobulins.
505
environment string. These frequencies are determined from a database of known protein structures and aligned sequences. The method determines the most favorable alignment of a target protein sequence to the residue positions defined by the environment string, and determines a best fit alignment score, Sij, for the target sequence. Each target sequence may then be further characterized by a ZScore, which is the number of standard deviations that Sij for the target sequence is above the mean alignment score for other target sequences of similar length.
5436850 METHOD
TO IDENTIFY
PROTEIN SEQUENCES THAT FOLD INTO A KNOWN THREE-DIMENSIONAL STRUCTURE
5437785 APPARATUS FOR DISSOLVED GAS FLOTATION IN ANAEROBIC WASTEWATER TREATMENT
Eisenberg David; Bowie James U; Luthy Rolan Los Angeles, CA, UNITED STATES assigned to The Regents of the University of California
Roshanravan Mel Coppell, TX, UNITED STATES assigned to Darling International
A computer-assisted method for identifying protein sequences that fold into a known three-dimensional structure. The inventive method attacks the inverse protein folding problem by finding target sequences that are most compatible with profiles representing the structural environments of the residues in known three-dimensional protein structures. The method starts with a known three-dimensional protein structure and determines three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chain area that is covered by polar atoms (O,N) or water, and (3) the local secondary structure. Based on these parameters, each residue position is categorized into an environment class. In this manner, a three-dimensional protein structure is converted into a one-dimensional environment string, which represents the environment class of each residue in the folded protein structure. A 3D structure profile table is then created containing score values that represent the frequency of finding any of the 20 common amino acids structures at each position of the
An apparatus for gas entrainment of wastewater in an anaerobic wastewater treatment system, the use of which includes the steps of withdrawing wastewater from an anaerobic digester and piping it into a flotation container. Thereafter the wastewater is pumped into a flee standing tank having pressure in the tank maintained at a predetermined level through the injection into the tank of compressed gas generated by anaerobic digestion occurring in the treatment system. The wastewater is removed from the tank and pumped through a multiple jet configuration wherein gas from the tank is entrained in the wastewater as the water is injected back into the tank. The gas entrained water is then discharged from the tank back into the flotation container where the gas bubbles particles to the surface of the water to form a sludge layer. The sludge layer formed on the surface of the water in the flotation container is recycled to the digester for further increased digestion, thereby providing an efficient flotation process with increased wastewater clarification, reduced disturbance of the anaerobic bacterial sludge layer, and efficient utilization of the gas generated by anaerobic digestion in the system.