US 6,363,399, Project-based full-length biomolecular sequence database with expression categories. Inventors: Timothy Maslyn, Janice Au-Young, Jennifer Hillman, Harold Hibbert, Ingrid Akerblom, Rachel Cheng, Yuanhua Tang. Assignee: Incyte Genomics.
Covers a relational database system for storing project-based biomolecular sequence information. The system catalogues sequence records along with identifying information about one or more projects to which they belong. The project-based system then permits users to obtain full-length biomolecular sequences from shorter sequences, according to the inventors.
US 6,370,479, Method and apparatus for extracting and evaluating mutually similar portions in one-dimensional sequences in molecules and/or three-dimensional structures of molecules. Inventors: Mayumi Tomikawa, Seiichi Aikawa, Fumiko Matsuzawa. Assignee: Fujitsu Limited.
Protects a method for similarity searching in three-dimensional molecular structures based on techniques used for one-dimensional sequences. Limiting conditions, such as the geometrical arrangements of elements, are added to homology searching, motif searching, and alignment methods to retrieve the three-dimensional structure and evaluate the functions of molecules. The technique then divides the molecules into secondary structures that are related to each other based on spatial similarity.
US 6,370,478, Methods for drug interaction prediction using biological response profiles. Inventors: Roland Stoughton, Sergey Stepaniants. Assignee: Rosetta Inpharmatics.
Provides several methods for detecting and predicting drug interaction. In one embodiment, for example, cellular constituents in a biological sample are monitored as the sample is subject to various drug treatments. The response of the cellular constituents is analyzed to detect interactions. It can be useful for predicting drug interactions in a model organism or for analyzing interaction between any perturbations in a biological system, according to the inventors.
US 6,377,893, Application of protein structure predictions. Inventor: Steven Benner. No Assignee.
Based on a previous method for modeling the folded structure of a set of proteins from the evolutionary analysis of a set of aligned homologous protein sequences, this patent covers methods for using these models. The first compares a predicted structure model for one family of proteins with a predicted structure model for a second family of proteins in order to detect homology based on the presence or absence of structural similarity flanking key residue motifs in the polypeptide sequence. The second method identifies mutations that are potentially adaptive by identifying episodes during the divergent evolution of a family of proteins where there is a high absolute rate of amino acid substitution. The third method identifies in vitro properties of a protein that are likely to play a physiological role in vivo. It synthesizes proteins having the reconstructed amino acid sequences of a protein before and after a period of rapid sequence evolution that characterizes adaptive substitution, measuring the in vitro properties of the protein before the episode of rapid sequence evolution. Then it measures the in vivo properties of the protein after the episode of rapid sequence evolution. According to Benner, the in vitro behaviors that remained unchanged through this episode are not likely to have adaptive significance physiologically, while the in vitro behaviors that did change are likely to have adaptive significance. The fourth method is a technique for organizing genome-sized sequence databases.