Abstract: A nanosensor for detecting molecule characteristics includes a membrane having an opening configured to permit a charged carbon nanotube to pass but to block a molecule attached to the carbon nanotube. The opening is filled with an electrolytic solution. An electric field generator is configured to generate an electric field relative to the opening to drive the charged carbon nanotubes through the opening. A sensor circuit is coupled to the electric field generator to sense current changes due to charged carbon nanotubes passing into the opening, and to bias the electric field generator to determine a critical voltage related to a force of separation between the carbon nanotube and the molecule.

Abstract: A nanosensor for detecting molecule characteristics includes a membrane having an opening configured to permit a charged molecule to pass but to block a protein molecule attached to a ligand connecting to the charged molecule, the opening being filled with an electrolytic solution. An electric field generator is configured to generate an electric field relative to the opening to drive the charged molecule through the opening. A sensor circuit is coupled to the electric field generator to sense current changes due to charged molecules passing into the opening. The current changes are employed to trigger a bias field increase to cause separation between the ligand and the protein to infer an interaction strength.

Abstract: A nanosensor for detecting molecule characteristics includes a membrane having an opening configured to permit a charged molecule to pass but to block a protein molecule attached to a ligand connecting to the charged molecule, the opening being filled with an electrolytic solution. An electric field generator is configured to generate an electric field relative to the opening to drive the charged molecule through the opening. A sensor circuit is coupled to the electric field generator to sense current changes due to charged molecules passing into the opening. The current changes are employed to trigger a bias field increase to cause separation between the ligand and the protein to infer an interaction strength.

Abstract: A mechanism is provided for ratcheting a double strand molecule. The double strand molecule is driven into a Y-channel of a membrane by a first voltage pulse. The Y-channel includes a stem and branches, and the branches are connected to the stem at a junction. The double strand molecule is slowed at the junction of the Y-channel based on the first voltage pulse being weaker than a force required to break a base pair of the double strand molecule. The double strand molecule is split into a first single strand and a second single strand by driving the double strand molecule into the junction of the Y-channel at a second voltage pulse.

Abstract: A mechanism is provided for ratcheting a double strand molecule. The double strand molecule is driven into a Y-channel of a membrane by a first voltage pulse. The Y-channel includes a stem and branches, and the branches are connected to the stem at a junction. The double strand molecule is slowed at the junction of the Y-channel based on the first voltage pulse being weaker than a force required to break a base pair of the double strand molecule. The double strand molecule is split into a first single strand and a second single strand by driving the double strand molecule into the junction of the Y-channel at a second voltage pulse.

Abstract: A computer assembly includes a processor configured to access data on a network and to perform a method. The method includes identifying, in the network, one or more references having a relevance level greater than a predetermined threshold. The one or more references are associated to one or more probe sequences corresponding to one or more biological sequences. The one or more probe sequences are ranked based on one or more criteria corresponding to a target biological sequence. The one or more probe sequences are assigned with a level of affinity to one or more segments of the target biological sequence based at least on the ranking of each of the one or more probe sequences.

Abstract: A method for associating data with a target biological sequence includes identifying, in a network, one or more references to data, where the data has a relevance level greater than a predetermined threshold. The method includes associating the one or more references to one or more probe sequences corresponding to a segment of a biological sequence to which the data pertains The one or more probe sequences are ranked based on one or more criteria and the probe sequences are assigned a level of affinity to a segment of the target biological sequence based at least on the ranking of each reference.

Abstract: A method, information processing system, and computer readable medium, are provided for analyzing a protein folding process. The method includes conducting an incremental pattern discovery process. The incremental pattern discovery process includes judging multidimensional data from a simulation of a protein folding process. The incremental pattern discovery process captures at least one intermediate data point in at least one pattern associated with the protein folding process.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: Techniques for protein structure analysis are provided. In one aspect, an apparatus for characterizing a multi-domain protein structure comprises the following steps. For at least one domain, a hydrophobic dipole, e.g., defined as a first-order hydrophobic moment of the domain, is calculated. A score representing the orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure is then calculated.

Abstract: Techniques for protein structure analysis are provided. In one aspect, a method of analyzing a multi-domain protein structure comprises the following steps. For at least one domain, a hydrophobic dipole, e.g., defined as a first-order hydrophobic moment of the domain, is calculated. A score representing the orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure is then calculated.

Abstract: Techniques for protein structure analysis are provided. In one aspect, an apparatus for characterizing a multi-domain protein structure comprises the following steps. For at least one domain, a hydrophobic dipole, e.g., defined as a first-order hydrophobic moment of the domain, is calculated. A score representing the orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure is then calculated.

Abstract: Techniques for protein structure analysis are provided. In one aspect, an apparatus for characterizing at least a portion of a protein structure comprising amino acid residues is provided. A set of values characterizing the protein structure are determined, wherein each value represents a distance from a center of the protein structure to a center of a given one or more of the amino acid residues. One or more other sets of values characterizing the hydrophobicity of the protein structure are obtained. A Fourier transform is performed on each of the sets of values to obtain transformed values sets. The transformed value sets are compared to correlate the hydrophobicity with the protein structure.

Abstract: Techniques for protein structure analysis are provided. In one aspect, an article of manufacture for characterizing at least a portion of a protein structure comprising amino acid residues is provided. A set of values characterizing the protein structure are determined, wherein each value represents a distance from a center of the protein structure to a center of a given one or more of the amino acid residues. One or more other sets of values characterizing the hydrophobicity of the protein structure are obtained. A Fourier transform is performed on each of the sets of values to obtain transformed values sets. The transformed value sets are compared to correlate the hydrophobicity with the protein structure.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: A method, information processing system, and computer readable medium, are provided for analyzing a protein folding process. The method includes conducting an incremental pattern discovery process. The incremental pattern discovery process includes judging multidimensional data from a simulation of a protein folding process. The incremental pattern discovery process captures at least one intermediate data point in at least one pattern associated with the protein folding process.

Abstract: A system and method for molecular dynamic simulation includes a database for storing data pertaining to at least one biomolecular system, a memory device for storing instructions for performing at least one algorithm having an electrostatic interaction calculating function and a multiple time step function, and subdividing forces on a basis of distance over which the forces act, and a processor for processing the data by executing the instructions in order to propagate the biomolecular system from a first set of coordinates to a second set of coordinates. The system and method significantly speed up the molecular dynamics simulation of biomolecular systems in which there are long-range and short-range electrostatic interactions and in which there are fast and slow motions, and make practicable the simulation of large protein solutions and thus, can be used to simulate protein folding and the binding of substrates to protein molecules.