Abstract: The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

Abstract: The present invention relates to a nanowire sensor and method for forming the same. More specifically, the nanowire sensor comprises at least one nanowire formed on a substrate, with a sensor receptor disposed on a surface of the nanowire, thereby forming a receptor-coated nanowire. The nanowire sensor can be arranged as a sensor sub-unit comprising a plurality of homogeneously receptor-coated nanowires. A plurality of sensor subunits can be formed to collectively comprise a nanowire sensor array. Each sensor subunit in the nanowire sensor array can be formed to sense a different stimulus, allowing a user to sense a plurality of stimuli. Additionally, each sensor subunit can be formed to sense the same stimuli through different aspects of the stimulus. The sensor array is fabricated through a variety of techniques, such as by creating nanopores on a substrate and electrodepositing nanowires within the nanopores.

Abstract: The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

Abstract: The present invention relates to a nanowire sensor and method for forming the same. More specifically, the nanowire sensor comprises at least one nanowire formed on a substrate, with a sensor receptor disposed on a surface of the nanowire, thereby forming a receptor-coated nanowire. The nanowire sensor can be arranged as a sensor sub-unit comprising a plurality of homogeneously receptor-coated nanowires. A plurality of sensor subunits can be formed to collectively comprise a nanowire sensor array. Each sensor subunit in the nanowire sensor array can be formed to sense a different stimulus, allowing a user to sense a plurality of stimuli. Additionally, each sensor subunit can be formed to sense the same stimuli through different aspects of the stimulus. The sensor array is fabricated through a variety of techniques, such as by creating nanopores on a substrate and electrodepositing nanowires within the nanopores.

Abstract: Computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the structure of transmembrane proteins such as G-Protein Coupled Receptors, and protein structural models generated according to the protocol. The protocol features a combination of coarse grain sampling methods, such as hydrophobicity analysis, followed by coarse grain molecular dynamics and atomic level molecular dynamics, including accurate continuum solvation, to provide a fast and accurate procedure for predicting GPCR tertiary structure.

Abstract: The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

Abstract: The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the structure of transmembrane proteins such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a combination of coarse grain sampling methods, such as hydrophobicity analysis, followed by coarse grain molecular dynamics and atomic level molecular dynamics, including accurate continuum solvation. Also included are energy optimization to determine the rotation of helices in the (seven-helical) TM bundle, and optimization of the helix translations along their axes and rotational optimization using hydrophobic moment of the helices, to provide a fast and accurate procedure for predicting GPCR tertiary structure.