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Recent Patents in Bioinformatics, July — August, 2008

US Patent 7,415,361. Methods and systems for analyzing and determining ligand-residue interaction. Inventors: Stephan Brunner; David Mosenkis; Frank Hollinger; William Chiang. Assignee: Locus Pharmaceuticals.
Protects a computer-based method for evaluating the free energy of binding between polypeptide amino acid residues and one or more molecular fragment types. The basis of the method is a weighted Metropolis Monte Carlo approach for sampling the grand canonical ensemble. “By making use of the properties of the grand canonical ensemble, the affinity of fragments for binding in the vicinity of each protein residue can be efficiently computed,” the patent abstract states. “The binding volume associated to each fragment-residue pair is estimated on the basis of a simple proximity criteria, and a useful affinity mapping of the protein surface can be obtained in this way.” The method can be used to identify protein binding sites or to identify key fragments used for building potential drug leads, according to the patent abstract.

US Patent 7,415,359. Methods and systems for the identification of components of mammalian biochemical networks as targets for therapeutic agents. Inventors: Colin Hill; Iya Khalil. Assignees: Gene Network Sciences, Cornell Research Foundation.
Protects methods for simulating cells and predicting cell states. As an example, the patent abstract states, the method can simulate a cellular biochemical network intrinsic to a phenotype of a cell by specifying its components and their interrelationships. These interrelationships can be represented with mathematical equations that can be solved to simulate a first state of the cell. “The simulated network can then be perturbed, and the equations representing the perturbed network can be solved to simulate a second state of the cell which can then be compared to the first state, identifying the effect of such perturbation on the network, and thereby identifying one or more components as targets,” according to the patent abstract. 

US Patent 7,415,358. Molecular toxicology modeling. Inventors: Donna Mendrick; Mark Porter; Kory Johnson; Brandon Higgs; Arthur Castle; Michael Elashoff. Assignee: Ocimum Biosolutions.
Predicts a method for elucidating global changes in gene expression and identifying toxicity markers in tissues or cells exposed to a known renal toxin. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.

US Patent 7,409,296. System and method for scoring peptide matches. Inventors: Jacques Colinge; Alexandre Masselot. Assignee: Geneva Bioinformatics.
Covers a method for scoring peptide matches that is based on an “appropriate signal detection based scoring system and what is believed to be the new concept of an extended match,” the patent abstract states. To score a match between two peptides, the method generates a stochastic model based on one or more match characteristics associated with the first peptide, the second peptide, and their fragments. “A first probability that the first peptide matches the second peptide, and second probability that the first peptide does not match the second peptide, may be calculated based on the stochastic model.” A match between the first peptide and the second peptide can be scored based on a ratio between the first probability and the second probability, according to the abstract.

US Patent 7,406,385. System and method for consensus-calling with per-base quality values for sample assemblies. Inventor: Jon Sorenson. Assignee: Applera (now Applied Biosystems).
Covers a software-implemented method for consensus base-call analysis used for sequence identification and quality assessment. The method uses quality values for a set of aligned sequence fragments to identify consensus base-calls and calculate associated consensus quality values. The method is applicable to resolution of single nucleotide polymorphisms, mixed-based sequences, heterozygous allelic variants, and heterogeneous polynucleotide samples, according to the patent abstract.

US Patent 7,406,384. System and method for identifying networks or ternary relationships in complex data systems. Inventor: Ker-Chau Li. Assignee: The Regents of the University of California.
Protects a method for identifying high-order associations between variables in complex systems that is “particularly useful where there is no correlation or weak correlation between variables due to the influence of a third variable, a ternary relationship,” the patent abstract states. In one embodiment applied to gene expression data, the activity of pairs of correlated genes due to the activity of one or more third genes is shown.

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