Abstract: The present invention provides a method and system for identifying, designing, and synthesizing proteins and protein backbones. The invention permits the qualitative identification of designable protein configurations and synthesis of protein folds. The method and system involve generating backbone protein configurations using a set of dihedral angle pairs, normalizing the total surface exposure of the configurations; generating a random set of sequences of hydrophobicities with uniform weight on the space of allowed sequences; determining, for each randomly generated sequence, which of the remaining configurations is the ground state; recording a ground-state configuration for each sequence wherein the desirable configurations are those containing the most sequences with that configuration as their ground state and finally, synthesizing sequences of amino acids for the desirable configurations.

Abstract: The present invention provides a method and system for identifying, designing, and synthesizing proteins and protein backbones. The invention permits the qualitative identification of designable protein configurations and synthesis of protein folds. The method and system involve generating backbone protein configurations using a set of dihedral angle pairs, normalizing the total surface exposure of the configurations; generating a random set of sequences of hydrophobicities with uniform weight on the space of allowed sequences; determining, for each randomly generated sequence, which of the remaining configurations is the ground state; recording a ground-state configuration for each sequence wherein the desirable configurations are those containing the most sequences with that configuration as their ground state and finally, synthesizing sequences of amino acids for the desirable configurations.

Abstract: Quorum-sensing bacteria communicate with extracellular signal molecules called autoinducers to allow community-wide synchronization of gene expression. The present invention relates to the identification the Vibrio harveyi and Vibrio cholerae protein Hfq as mediating interactions between small, regulatory RNAs (sRNAs) and specific messenger RNA (mRNA) targets. Accordingly, the present invention provides nucleic acids encoding the Vibrio sRNAs, strains having various deletions and mutations of one or more qrr genes encoding these sRNA as well as methods of identifying quorum-sensing regulators. Additionally, the invention relates to an isolated V. harveyi Hfq protein and conservative amino acid substitutions thereof as well as nucleic acids encoding those proteins, recombinant methods of producing those proteins and antibodies against those proteins.

Abstract: The present invention relates to a method for quantitative design and optimization of polymers. More specifically, the present invention relates to method for calculating the solvent-exposed area of a polymer.