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Recent Patents in Bioinformatics, April — May 2007

US Patent 7,215,804. Method and apparatus for providing a bioinformatics database. Inventors: David Balaban, Arun Aggarwal. Assignee: Affymetrix.
The patent protects a method for organizing information relating to polymer probe array chips, including oligonucleotide array chips. The patent abstract describes a database model that organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, and expression analysis of chip results, etc. The model is “readily translatable” into database languages such as SQL, according to the patent abstract, and scales to permit mass processing of probe array chips.

US Patent 7,212,951. Method for characterizing and analyzing 3-D shapes of molecules utilizing steric multiplets. Inventors: Edmond Abrahamian, Robert Clark, Peter Fox, Essam Metwally. Assignee: Tripos.
The patent abstract describes a method for representing steric features in the three-dimensional disposition of atoms in molecules as “multiplets” using a defined set of steric descriptors. The resulting multiplets can be encoded in bitmaps, which can be generated in compressed form and used to compare individual conformers or ensembles of conformers of molecules to each other without decompression. These comparisons are useful in molecular similarity analysis, in molecular diversity analysis, in database searching, and in conformational analysis, the abstract states.

US Patent 7,212,924. Method of inferring three-dimensional structure of protein. Inventor: Akiko Itai. Assignee: None.
The patent abstract describes a method of predicting a scaffold of a protein based on a query sequence. The method uses a database containing information on the side chain of each amino acid residue contained in the sequence of each reference protein whose three-dimensional structure is known. The method chooses at least one template protein among the reference proteins that has high similarity in three-dimensional structure to the protein comprising the query sequence, and predicts the scaffold of the protein comprising the query sequence.

US Patent 7,211,388. Method for profiling and identifying persons by using data samples. Inventors: Howard Cash, Simon Mercer, Jonathon Hoyle, Lucy Hadden, Amy Sutton, David Relyea, William Wake, Matthew Smith, Tom Kubit, Greg Poth, Anna Korn, Anna Khizhnyak, Tracy Beeson. Assignee: Gene Codes Forensics.

The patent abstract describes a method for profiling and identifying persons by using data samples. The method uses a list of one or more aggregated matching samples with consistent STR profiles. A method for aggregating samples from a plurality of disparate samples, and combining the aggregated samples is also provided.

Filed under

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.