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IP Update: Jun 18, 2010

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Recent Patents in Bioinformatics, April — June 2010

US Patent 7,739,091. Method for estimating protein-protein binding affinities. Inventor: Joseph Audie. Assignee: The Research Foundation of State University of New York.

Describes a computational method for predicting the binding affinity between two molecular entities. The method evaluates the free energy of binding to predict the binding affinity between the molecular entities.


US Patent 7,739,055. Methods and systems for generating and evaluating peptides. Inventors: Gregory Stephanopoulos, Kyle Jensen, Christopher Loose. Assignee: Massachusetts Institute of Technology.

Protects methods to create databases of peptides having a desirable property, such as antimicrobial activity. The method involves first analyzing a database of known peptides for a pattern statistically associated with the desirable property. "Once the database is identified, the database may be processed in a pattern recognition procedure that identifies a set of patterns that may be representative of a peptide having the desirable property," the patent abstract states. "A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or similarity between one or more of the new sequences and the set of identified patterns."


US Patent 7,739,053. System and process of determining a biological pathway based on a treatment of a biological specimen. Inventors: Peter Palenchar, Dennis Shasha, Michael Chou, Marc Rejali, Yair Dorsett, Andrei Kouranov, Gloria Coruzzi. Assignee: New York University.

Describes a computational system and method for analyzing transcriptome profiles, metabolome profiles, proteome profiles, "or any combination thereof to determine the biochemical pathways affected by a treatment," according to the patent abstract. The system and method "may allow users to query the pathways generated and to filter the results of queries based on the -omic profile data, pathways involving molecules of interest, notions of biochemical importance, milestone molecules, and other factors."


US Patent 7,734,427. System, method, and computer program for non-binary sequence comparison. Inventor: Jeffrey Clark. Assignee: Bioinformatica.

Describes a system and method for performing non-binary comparison of biological sequences that includes a new non-binary counting measure that obtains "substantially more information about sequences and comparisons between them than is gathered by conventional bioinformatics techniques," according to the patent abstract.


US Patent 7,734,425. Apparatus and method for searching protein active site. Inventors: Dae Hee Kim, Sung Hee Park, Chan Yong Park, Seon Hee Park. Assignee: Electronics and Telecommunications Research Institute.

Protects a method of searching a protein active site that includes a database that stores information on reference active sites, a "comparing unit," that calculates 3D structural similarities according to the number of overlapping residues, and a "search unit" that searches the reference active site with respect to the input active site according to the similarities. "Similar active sites can be searched with a low computational complexity, [and] thereby … used for a correct new drug design," the abstract states.


US Patent 7,734,423. Method, system, and apparatus for virtual modeling of biological tissue with adaptive emergent functionality. Inventors: William Crowley Jr., Ullysses Eoff, Cap Petschulat, Mason Vail, Richard Newman, Timothy Andersen, Timothy Otter, Robert Davis. Assignee: Crowley Davis Research.

Describes a computational system for modeling biological tissue that yields "virtual multicellular individuals that exhibit adaptive emergent functionality in response to environmental stimuli," according to the patent abstract. The method generates virtual environmental parameters and cells with genomes that are modified by genetic operations. "Cells are developed into generations of multicellular individuals, which are evaluated and selected via evolutionary search according to fitness criteria, and individuals exhibiting adaptive emergent functionality, such as self-repair, are developed and identified," the abstract states.


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US Patent 7,734,421. Method for identifying motifs and/or combinations of motifs having a Boolean state of predetermined mutation in a set of sequences and its applications. Inventors: Anne Vanet, Michaela Muller-Trutwin, Thomas Valere. Assignee: Centre National de la Recherche Scientifique.

Covers a method for identifying a motif or a combination of motifs having a Boolean state of predetermined mutations in a set of sequences. The method first aligns a set of sequences of ordered motifs, then compares a reference sequence with the set of aligned sequences and identifies motifs "not having mutated simultaneously or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of the set."


US Patent 7,734,420. Methods and systems to identify operational reaction pathways. Inventors: Bernhard Palsson, Markus Covert, Markus Herrgard. Assignee: the Regents of the University of California.

Describes a method for identifying an operational reaction pathway of a biosystem. The method first provides a set of systemic reaction pathways through a reaction network that represents the biosystem, provides a set of phenomenological reaction pathways of the biosystem, and then compares the systemic reaction pathways with the phenomenological reaction pathways, "wherein a pathway common to said sets is an operational reaction pathway of said biosystem." The patent also describes a method of refining a biosystem reaction network, a method of reconciling biosystem data sets, a method of determining the effect of a genetic polymorphism on whole cell function, and a method of diagnosing a genetic polymorphism-mediated pathology.


US Patent 7,720,614. Method for identification of cis-regulatory modules via computational analysis of single polynucleotide polymorphisms (SNPs) and insertions/deletions (indels). Inventors: Eric Davidson, Robert Cameron. Assignee: California Institute of Technology.

Describes a computational method that uses the process of cis-regulatory module evolution to identify conserved sequence patches that exhibit suppression of change by SNP/indel occurrence. The method determines sequence similarities that are significantly greater than random expectation on selected genome sequences from two or more species in sequences that lie outside of protein coding regions, sorts the similarities for conserved patches of SNPs and indels, and selects such patches to identify cis-regulatory modules.


US Patent 7,711,491. Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis. Inventors: Jennifer Vandersall, Shea Gardner, David Clague. Assignee: Lawrence Livermore National Security.

Protects a computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method include modules that address the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, "which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species," according to the patent abstract.


US Patent 7,702,465. Method, computing routine, device for predicting properties of MHC/peptide complexes, and data and peptides produced therefrom. Inventors: Ignace Lasters, Johan Desmet. Assignee: Algonomics.

Covers a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility class I and class II molecules. "The properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor," the abstract states. The invention also describes a computer program and data produced by the invention.


US Patent 7,702,464. Method and apparatus for codon determining. Inventors: Robin Emig, Richard John Fox, Claes Gustafsson, Sridhar Govindarajan, Jeremy Minshull, Guy Cavet. Assignee: Maxygen.

Describes computer-based methods for minimizing and/or optimizing data strings. "Minimized data strings can represent data sequences important in certain biologic analyses and/or syntheses," according to the patent abstract. "In specific embodiments, a request is generated by a user at a client system and received by a server system. The server system accesses initial data indicated or provided by the client system. The server system then performs an analysis to minimize the data needed for further reactions."


US Patent 7,702,104. System and method for securing genomic information. Inventors: Virinder Mohan Batra, Mine Altunay, Chetna Dnyandeo Warade, Daniel Colonnese, Lindsay Kathleen Wilber, Satyaprasad Vadlamudi. Assignee: International Business Machines.

Describes a system and method for securing an electronic transmission of a nucleotide chain. The method includes a system for identifying coding and non-coding regions in the nucleotide chain and a system for selectively encrypting only the coding regions identified in the nucleotide chain.


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PNAS Papers on CRISPR-Edited Cancer Models, Multiple Sclerosis Neuroinflammation, Parasitic Wasps

In PNAS this week: gene-editing approach for developing cancer models, role of extracellular proteins in multiple sclerosis, and more.