In Silico Screening Patents (Class 506/8)
  • Publication number: 20130102480
    Abstract: The present invention provides a prediction device, a prediction method, a program, and a recording medium, with which whether or not desired aptamer sequences are enriched can be predicted easily. The prediction device of the present invention 10 includes an input unit 11, a calculation unit 12, and a prediction unit 13. The input unit 11 is a unit through which sequence information on a target aptamer sequence group including selected aptamers in a target pool and a reference aptamer sequence group including reference aptamer sequences are inputted. The calculation unit 12 calculates the free energy of the target aptamer sequence group and the free energy of the reference aptamer sequence group. The prediction unit 13 compares the free energy of these sequence groups, and predicts that the target pool is an enriched pool when the free energy of the target aptamer sequence group is lower than the free energy of the reference aptamer sequence group.
    Type: Application
    Filed: July 2, 2011
    Publication date: April 25, 2013
    Inventors: Jou Akitomi, Shintarou Katou, Shotaro Tsuji, Takashi Ohtsu, Iwao Waga
  • Publication number: 20130096017
    Abstract: Motility contrast imaging (MCI) is a depth-resolved holographic technique to extract cellular and subcellular motion inside tissue. The holographic basis of the measurement technique makes it highly susceptible to mechanical motion. The motility contrast application, in particular, preferably includes increased mechanical stability because the signal is based on time-varying changes caused by cellular motion, not to be confused with mechanical motion of the system. The use of the resulting spectrogram response signatures, or “fingerprint” data, of known compounds is disclosed to screen new compounds for leads as to those having potentially beneficial mechanisms of action. The “fingerprint” data of known toxic compounds can be used to screen new compounds for toxicity.
    Type: Application
    Filed: June 17, 2011
    Publication date: April 18, 2013
    Inventors: David D. Nolte, Kwan Jeong
  • Publication number: 20130084641
    Abstract: The present invention provides a method of selecting a mRNA for production of a polypeptide of interest comprising: a) producing an array of individual mRNA sequences comprising different nucleotide sequences encoding the polypeptide of interest; b) determining one or more or two or more of the following parameters for each individual mRNA sequence of (a): (i) minimum free energy (MFE) RNA secondary structure; (ii) ensemble free energy (EFE); (iii) frequency of the minimum free energy (FMFE) RNA secondary structure in a thermodynamic ensemble; and (iv) ensemble diversity (ED); c) ranking the individual mRNA sequences of the array according the parameters determined in step (b); and d) selecting a mRNA sequence from the ranked array of step (c), wherein the selected mRNA produces the polypeptide of interest. The present invention further provides a method of selecting a mRNA for enhanced and reduced production of a polypeptide of interest.
    Type: Application
    Filed: December 7, 2012
    Publication date: April 4, 2013
    Applicant: Syngenta Participations AG
    Inventors: Shib Sankar Basu, Kristern Kamerath Dang, Kasimalai Azhakanandam, Thomas Z. McNeill, Sheng Guo
  • Publication number: 20130079233
    Abstract: Methods and systems for predicting coreceptor tropism are provided. In certain embodiments, the methods may include obtaining the amino acid and/or nucleic acid sequence of at least a portion of the envelope or envelope coding region from a biological sample obtained from a subject; analyzing the amino acid sequence, nucleic acid sequence, or both of the portion of the envelope or envelope coding region using a case based reasoning analysis; and determining the coreceptor tropism. Also provided are systems and computer readable media for utilizing the systems or performing the methods are disclosed.
    Type: Application
    Filed: September 24, 2012
    Publication date: March 28, 2013
    Applicant: Laboratory Corporation of America Holdings
    Inventor: Laboratory Corporation of America Holdings
  • Publication number: 20130053259
    Abstract: The invention provides methods of using sequence based analysis and rational strategies to modify and improve the structural and biophysical properties of single chain antibodies (scFvs), including stability, solubility, and antigen binding affinity. These methods and strategies can be used individually or in combination. The methods of the present invention also include the use of a database comprising scFv sequences from an experimentally screened scFv library of antibodies that have been selected to have superior solubility and stability. The invention also provides methods of using the properties found for these selected antibodies in a general approach for reshaping scFv antibodies to improve stability and solubility properties of a single chain antibody fragment.
    Type: Application
    Filed: August 23, 2012
    Publication date: February 28, 2013
    Inventors: David M. Urech, Leonardo Borras
  • Publication number: 20130045878
    Abstract: Processes are described that include computational tools for identification of unknown pathogenic organisms and other threat agents (e.g., rare variants) in samples. The processes can be conducted without specific a priori knowledge of the unknown. Identification may include fragmenting a genome from one or more candidate organisms and READs and/or CONTIGs segments for the unknown organism in silico to form fragments, and determining the statistical relevance of exact fragment matches between the sample fragments and the candidate fragments.
    Type: Application
    Filed: May 31, 2012
    Publication date: February 21, 2013
    Inventors: Lee Ann McCue, Bobbie-Jo M. Webb-Robertson
  • Publication number: 20130046076
    Abstract: Present invention disclosed three-dimensional crystal structure of N-terminus polypeptide of influenza virus polymerase subunit (PA_N). PA_N is residues 1˜50 to 150˜300 of influenza virus polymerase subunit PA. In three-dimensional structure, at least 40% of atoms showed same atomic coordinates, compared to that listed in Table. In other words, in three-dimensional structure of influenza virus polymerase subunit PA_N, 40% of atomic coordinates on carbon skeleton of residues of influenza virus polymerase subunit PA_N, showed less than or equal to 1.7 ? of average variance, compared to the atomic coordinates listed in Table1. Present invention also disclosed the expression, purification, crystallization methods, and three-dimensional crystal structure of 256 residues in the N-terminus of influenza virus polymerase subunit PA, and applications of the crystal structure on drug screening and designing.
    Type: Application
    Filed: February 3, 2010
    Publication date: February 21, 2013
    Applicant: Institute of Biophysics Chinese Academy of Sciences
    Inventors: Yingfang Liu, Zihe Rao
  • Publication number: 20130035244
    Abstract: The invention relates to a method for characterising three-dimensional objects, including steps comprising: i) generating a three-dimensional reconstruction of a three-dimensional object; ii) generating a mesh of the object, said mesh being made up of points connected two-by-two by a ridge; iii) characterising the points and/or faces of the mesh of the object according to the statuses of remarkable properties at said points; iv) splitting the object into contiguous three-dimensional regions based on the mesh and the characterisation of the points thereof; v) creating a database of regions that represent objects of an environment; and/or vi) screening a region on a database in order to find objects that contain similar and/or complementary regions; and/or vii) inferring functions of the objects according to similarities in the regions thereof; and/or viii) inferring interactions between objects by complementarity of the regions thereof; and/or ix) specifying the frequency of a region in an environment.
    Type: Application
    Filed: July 26, 2010
    Publication date: February 7, 2013
    Applicant: BIONEXT S.A.
    Inventor: Laurent Philippe Albou
  • Publication number: 20130005590
    Abstract: Methods for design of genetic circuits are provided.
    Type: Application
    Filed: June 5, 2012
    Publication date: January 3, 2013
    Applicant: The Regents of the University of California
    Inventors: Chunbo Lou, Tae Seok Moon, Virgil Rhodius, Brynne Stanton, Alvin Tamsir, Karsten Temme, Chirs Voigt
  • Publication number: 20120322671
    Abstract: Methods and systems for assessing the probabilities of the expression of one or more traits in progeny are described.
    Type: Application
    Filed: August 22, 2012
    Publication date: December 20, 2012
    Applicant: GenePeeks, Inc.
    Inventor: Lee M. SILVER
  • Publication number: 20120322717
    Abstract: The present invention relates to the field of therapeutic methods to screen for compounds on the basis of their ability to influence Wnt activity. The screening process is applied to both a physical library of a series of compounds and a virtual library of compounds that affect Wnt activity. In one aspect, the virtual screening process could be carried out where a permutational library of small peptides is substituted for the small organic molecules. The inventive methods may be used to empirically test for effects on Wnt activity and may also be applied to any pair of proteins involved in protein-protein interactions.
    Type: Application
    Filed: May 22, 2009
    Publication date: December 20, 2012
    Inventors: Dakai Liu, Xiaofeng Li, Richard Jin, Yuaxin Liang, Wei Cheng, Riddhi Bhattacharyya, Guangrong Zhang
  • Publication number: 20120309759
    Abstract: The present invention embraces methods for identifying compounds that modulate the activity of telomerase. Compounds of the invention are identified by designing or screening for a compound which binds to at least one amino acid residue of the TRBD, “thumb,” “finger,” and/or “palm” domain; or FP-pocket, PT-pocket or Th-pocket of telomerase and testing the compound for its ability to modulate the activity of telomerase. Compounds selected for interacting with the T-pocket or Fingers-Palm pocket of telomerase are also provided.
    Type: Application
    Filed: February 8, 2011
    Publication date: December 6, 2012
    Applicant: The Wistar Institute
    Inventor: Emmanuel Skordalakes
  • Publication number: 20120295796
    Abstract: A system and method of identifying a target molecule that bind to the bioactive site of a protein or protein complex is described. The system and method includes the steps of calculating the information signature of a first molecule that is known to bind to the bioactive site of a protein or protein complex, wherein the information signature is a string of numerical values based on the average distance and physico-chemical properties of each atom of a plurality of atoms in the first molecule, calculating the information signature of each target molecule in a library of target molecules, comparing the information signature of the first molecule to the information signatures of the target molecules, and selecting the target molecules having an information signature that is similar to the information signature of the first molecule.
    Type: Application
    Filed: September 6, 2011
    Publication date: November 22, 2012
    Inventors: Gerald J. Wyckoff, Brian Moldover, Lisa Kenney, Ada Solidar, Jeff Murphy
  • Publication number: 20120289417
    Abstract: The invention relates to databases of T cell epitopes, especially helper T cell epitopes, for rapid interrogation of protein sequences for the presence of T cell epitopes. The invention includes full or partial databases and data structures of T cell epitopes including epitopes identified especially by ex vivo T cell assays with test peptides and includes T cell epitopes identified by extrapolation of data from test peptides. The present invention also includes high throughput methods for determining the T cell epitope activity of peptides for subsequent inclusion in databases and data structures including methods where subsets of T cell especially regulatory T cells are removed or inhibited from T cell assays in order to maximize the sensitivity of detection of T cell epitope activity.
    Type: Application
    Filed: July 31, 2012
    Publication date: November 15, 2012
    Inventors: Frank Carr, Matthew Paul Baker
  • Publication number: 20120283112
    Abstract: Provided are methods and systems for determining functional relationships between a cosmetic agent and a skin tissue condition of interest. Also provided are methods and systems for identifying cosmetic agents that affect a skin aging tissue condition, as well as the use of agents identified by such methods and systems for the preparation of cosmetic compositions, personal care products, or both.
    Type: Application
    Filed: February 22, 2012
    Publication date: November 8, 2012
    Inventors: Robert Lloyd Binder, Robert Scott Youngquist, Jun Xu, Kenton Duane Juhlin, Rosemarie Osborne, Scott Michael Hartman
  • Publication number: 20120264942
    Abstract: Provided is a compound found by screening a material for inhibiting an osteopontin, in which the material for inhibiting the osteopontin can increase effectiveness as an excellent material for inhibiting an osteoporosis.
    Type: Application
    Filed: November 14, 2011
    Publication date: October 18, 2012
    Inventors: In-Cheol Kang, Eung-Yoon Kim, Young-Jin Choi
  • Publication number: 20120258875
    Abstract: The invention provides methods and apparatus for characterizing complex polymeric mixture of interest. Candidate solutions are eliminated from a solution space using one or more experimental measurements of a polymeric mixture of interest. The elimination step can be repeated one or more times using different experimental measurements produced by various chemical and physical protocols, so that the remaining candidate solutions converge to describe the actual polymeric mixture under investigation. Once the composition of the complex polymeric mixture has been characterized, the information thus generated can be used to facilitate, for example, the manufacture of a bio-equivalent of the complex polymeric mixture.
    Type: Application
    Filed: March 20, 2012
    Publication date: October 11, 2012
    Inventor: Sasisekharan Raguram
  • Publication number: 20120258874
    Abstract: Described herein is a discovery Platform Technology for analyzing a biological system or process (e.g., a disease condition, such as cancer) via model building.
    Type: Application
    Filed: March 2, 2012
    Publication date: October 11, 2012
  • Publication number: 20120252683
    Abstract: A method of scoring binding affinity of a proposed ligand molecule for a receptor molecule using a computer and computer data bases, which accounts for the increase in energy required where docking disrupts water molecules that are localized at ligand hydration sites. The method uses computer-stored data representing a predicted ligand-receptor structure (preferably one that is validated). The computerized scoring analysis includes determining whether the receptor includes one or more hydration sites occupied by localized water, and, if so, assessing a penalty if docking the ligand into the receptor results in unfavorable interaction of the ligand with a localized water molecule remaining at the receptor hydration site (i.e. after docking).
    Type: Application
    Filed: April 4, 2011
    Publication date: October 4, 2012
    Inventors: Richard A. Friesner, Robert Murphy
  • Publication number: 20120252684
    Abstract: In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.
    Type: Application
    Filed: March 29, 2012
    Publication date: October 4, 2012
    Inventors: Sergey A. Selifonov, Willem P.C. Stemmer
  • Publication number: 20120220469
    Abstract: This invention provides methods and systems for identifying and typing toxicity of chemical compositions, as well as for screening new compositions for toxicity. The invention involves detecting alterations in gene or protein expression and hence establishing molecular profiles in isolated mammalian LSCs contacted with various chemical compositions of known and unknown toxicities, and correlating the molecular profiles with toxicities of the chemical compositions.
    Type: Application
    Filed: February 21, 2012
    Publication date: August 30, 2012
    Applicant: VistaGen Therapeutics, Inc.
    Inventor: H. Ralph SNODGRASS
  • Publication number: 20120220472
    Abstract: There is disclosed a method of extracting large scale biological, biochemical or molecular information about an index disease, biological state, or systems from imaging by correlating the imaging features associated with said disease, state or system with corresponding large scale biological data.
    Type: Application
    Filed: February 27, 2012
    Publication date: August 30, 2012
    Applicant: IMAGENEDX, INC.
    Inventor: Michael D. Kuo
  • Publication number: 20120202699
    Abstract: The present invention relates to the determination of intra- or intermolecular interaction between molecules in aqueous solution, the method comprising the steps of: (a) determining the dehydration of all atoms in the intermolecular interface, (b) adding the vacuum hydrogen bond energy, and (c) further adding the change in the free enthalpy of the interacting partners upon their interaction. The obtained results can be used for the prediction if and to what extent two molecules of various origin fit to each other.
    Type: Application
    Filed: February 6, 2012
    Publication date: August 9, 2012
    Inventors: Gudrun Lange, Robert Klein, Juergen Albrecht, Matthias Rarey, Ingo Reulecke
  • Publication number: 20120184616
    Abstract: The present invention relates to the field of therapeutic methods, compositions and uses thereof, that affect, directly or indirectly, the behavior of LRP receptors. These compositions and methods result in the treatment of inflammatory, immunological and metabolic conditions. More particularly, the methods and compositions of the invention are directed to the identification of small molecules, drugs and/or pharmacological agents that affect the Wnt pathway by affecting normal complex formation among various signaling receptors, the LRP5 and LRP6 receptor, and related ligands.
    Type: Application
    Filed: August 7, 2008
    Publication date: July 19, 2012
    Inventors: Elazar Rabbani, Xiaofeng Li, Dakai Liu, Yazhou Zhang, Richard Jin, Riddhi Bhattacharyya, Wei Cheng, James J. Donegan
  • Publication number: 20120178747
    Abstract: The mechanism by which the high bone mass (HBM) mutation (G171V) of the Wnt coreceptor LRP5 regulates the canonical Wnt signaling was investigated. The mutation was previously shown to reduce Dkk protein-1-mediated antagonism, suggesting that the first YWTD repeat domain where G171 is located may be responsible for Dkk protein-mediated antagonism. However, we found that the third YWTD repeat, but not the first repeat domain, is required for DKK1-mediated antagonism. Instead, we found that the G171V mutation disrupted the interaction of LRP5 with Mesd, a chaperon protein for LRP5/6 that is required for the coreceptors' transport to cell surfaces, resulting in less LRP5 molecules on the cell surface. Although the reduction in the level of cell surface LRP5 molecules led to a reduction in Wnt signaling in a paracrine paradigm, the mutation did not appear to affect the activity of coexpressed Wnt in an autocrine paradigm.
    Type: Application
    Filed: November 14, 2006
    Publication date: July 12, 2012
    Inventors: Dianqing (Dan) Wu, Dakai Liu, James J. Donegan
  • Publication number: 20120178697
    Abstract: The Wnt signaling pathways are involved in embryo development as well as in tumorigenesis. Dishevelled (Dvl) tranduces Wnt signals from the receptor Frizzled (Fz) to downstream components in canonical and non-canonical Wnt signaling pathways, and the Dvl PDZ domain plays an essential role in both pathways, and the Dvl PDZ domain binds directly to Fz receptors. In the present invention using NMR-assisted virtual ligand screening, several compounds were identified and were found to bind to the Dvl PDZ domain. Molecular dynamics simulation was used to analyze the binding between the PDZ domain and these compounds in detail. These compounds provide a basis for rational design of high-affinity inhibitors of the PDZ domain, which can block Wnt signaling by interrupting the Fz-Dvl interaction.
    Type: Application
    Filed: April 1, 2005
    Publication date: July 12, 2012
    Inventors: Jie Zheng, Jufang Shan, Dianqing Wu
  • Patent number: 8198218
    Abstract: Heterocyclic compounds having a relatively flexible backbone are used to create combinatorial libraries that permit screening for lead compounds and selection of drug candidates for a variety of uses in human and veterinary medicine as well as in agriculture. The compounds of the library generally differ in ring size and chirality of substituents on the ring. Also disclosed are methods for providing and screening these libraries, preferably in an automated or computerizable manner, such as by using a computer program to virtually screen the compounds in order to identify those that are predicted to have bioactive conformations that should give rise to desirable biological effects.
    Type: Grant
    Filed: May 29, 2009
    Date of Patent: June 12, 2012
    Assignee: Yissum Research Development Company of the Hebrew University of Jerusalem
    Inventor: Chaim Gilon
  • Publication number: 20120142623
    Abstract: Compositions and methods are provided for predicting inhibitors of protein targets related to treatment of infectious disease, for example, bacterial, viral, or parasitic diseases. Methods are provided for predicting inhibitors of protein targets related to treatment infectious disease, for example, microbial disease, utilizing a docking with dynamics protocol to identify inhibitors, or utilizing a protein structure energy function to identify peptide or peptidomimetic inhibitors.
    Type: Application
    Filed: July 6, 2007
    Publication date: June 7, 2012
    Inventors: Michael Lagunoff, Wesley C. Van Voorhis, Ekachai Jenwitheesuk, Ram Samudrala
  • Publication number: 20120122712
    Abstract: A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods.
    Type: Application
    Filed: November 9, 2011
    Publication date: May 17, 2012
    Inventor: Peter H. Goldstein
  • Publication number: 20120108791
    Abstract: Rotamer libraries and methods of use thereof are provided.
    Type: Application
    Filed: April 20, 2010
    Publication date: May 3, 2012
    Inventors: Roland Dunbrack, Maxim Shapovalov
  • Publication number: 20120107285
    Abstract: Certain embodiments disclosed herein include, but are not limited to, at least one of compositions, methods, devices, systems, kits, or products regarding rejuvenation or preservation of stem cells. Certain embodiments disclosed herein include, but are not limited to, methods of modifying stem cells, or methods of administering modified stem cells to at least one biological tissue.
    Type: Application
    Filed: October 28, 2010
    Publication date: May 3, 2012
    Inventors: Roderick A. Hyde, Lowell L. Wood, JR.
  • Publication number: 20120108448
    Abstract: Systems and method for curation of mass spectral libraries. In general, the systems and methods provided herein (a) obtain an experimentally derived mass spectrum of a compound of interest; (b) identify a peak in the mass spectrum that represent an experimental m/z value for an ion fragment of the compound of interest; (c) remove from the mass spectrum any peak that does not correspond to the compound of interest; and (d) replace the experimental m/z value for the peak identified in step (b) with a calculated theoretical m/z value for the ion fragment.
    Type: Application
    Filed: November 3, 2010
    Publication date: May 3, 2012
    Inventors: Frank E. Kuhlmann, Heloise Logan, Steven M. Fischer, Xiangdong Don Li
  • Publication number: 20120108449
    Abstract: A crystal comprising human isoglutaminyl cyclase having a characterised space group of P1211 and unit cell dimensions of +/?5% of a=126.51 ?, b=109.68 ?, c=159.53 ?, ?=90.0°, ?=104.9° and ?=90.0°.
    Type: Application
    Filed: October 28, 2011
    Publication date: May 3, 2012
    Applicant: PROBIODRUG AG
    Inventors: Anett Stephan, Stephan Schilling, Jens-Ulrich Rahfeld, Michael Wermann, Christoph Parthier, Hans-Ulrich Demuth, David Ruiz-Carillo, Milton T. Stubbs
  • Publication number: 20120101284
    Abstract: There is provided a compound found by screening a material for inhibiting a binding between a beta-amyloid 1-42 peptide and VEGF165, in which the inhibition material screened according to the present invention can improve effectiveness as a material for treating Alzheimer's disease.
    Type: Application
    Filed: June 15, 2010
    Publication date: April 26, 2012
    Inventors: In-Cheol Kang, Chan-Won Park
  • Publication number: 20120083418
    Abstract: A method for designing primers, being capable of efficiently designing primers for a SELEX method is provided. The method for designing primers of the present invention includes the steps of: (S1) generating candidate primer sequences; (S2) evaluating the candidate primer sequences according to a predetermined criterion so as to select candidate primer sequences; (S3) based on the selected candidate primer sequences, generating random pools each containing a plurality of nucleic acid sequences that include random sequences and the candidate primer sequences; (S4) predicting a structure of each of the nucleic acid sequences in each of the random pools and evaluating the predicted structure according to a predetermined criterion so as to select a random pool; and (S5) determining that the candidate primer sequences in the selected random pool are employed as primer sequences. The respective steps are carried out using a computer.
    Type: Application
    Filed: March 26, 2010
    Publication date: April 5, 2012
    Applicant: NEC SOFT, LTD.
    Inventors: Jou Akitomi, Shintarou Katou, Yoshihito Yoshida
  • Publication number: 20120071333
    Abstract: Disclosed herein are systems and uses of systems operating between fully quantum coherent and fully classical states. Such systems operate in what is termed the “Poised realm” and exhibit unique behaviors that can be applied to a number of useful applications.
    Type: Application
    Filed: July 20, 2011
    Publication date: March 22, 2012
    Inventors: Stuart Kauffman, Samuli Niiranen, Gábor Vattay
  • Publication number: 20120065208
    Abstract: A method for treating, preventing or ameliorating a hyperliferative disease and/or disorder in a mammal, comprises administering a therapeutically effective amount of one or more compounds selected from the group consisting of a compound of Formula (III), a compound of Formula (IV), and a pharmaceutically acceptable salt of Formula (III) or Formula (IV): wherein R2 is selected from the group consisting of methyl, ethyl, n-propyl, isopropyl, n-butyl, vinyl and allyl.
    Type: Application
    Filed: September 28, 2011
    Publication date: March 15, 2012
    Inventors: Gilles Klopman, Suman K. Chakravarti
  • Publication number: 20120058905
    Abstract: Naturally-occurring and modified recombinant nucleic acid molecules have been isolated that encode linear pre-cursors of cyclopeptides of the Caryophyllaceae (Ccps) and Caryophyllaceae-like (Clcps) type V1 class of cyclopeptides. Such nucleic acid molecules are useful for producing cyclopeptides and their linear precursors by recombinant methods.
    Type: Application
    Filed: May 10, 2010
    Publication date: March 8, 2012
    Inventors: Patrick S. Covello, Raju S.S. Datla, Sandra Lee Stone, J. John Balsevich, Martin John Reaney, Paul Grenville Arnison, Janet Anne Condie
  • Publication number: 20120053067
    Abstract: The invention describes an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a large molecule for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment:large molecule interactions. The FragMaps may be used to qualitatively inform the design of small-molecule ligands or as scoring grids for high-throughput in silico docking that incorporates both an atomic-level description of solvation and the large molecule's flexibility.
    Type: Application
    Filed: April 29, 2010
    Publication date: March 1, 2012
    Inventors: Alexander D. MacKerell, JR., Olgun Guvench
  • Publication number: 20120054922
    Abstract: The invention relates to methods for the identification and use of introns with gene expression enhancing properties. The teaching of this invention enables the identification of introns causing intron-mediated enhancement (IME) of gene expression. The invention furthermore relates to recombinant expression construct and vectors comprising said IME-introns operably linked with a promoter sequence and a nucleic acid sequence. The present invention also relates to transgenic plants and plant cells transformed with these recombinant expression constructs or vectors, to cultures, parts or propagation material derived there from, and to the use of same for the preparation of foodstuffs, animal feeds, seed, pharmaceuticals or fine chemicals, to improve plant biomass, yield, or provide desirable phenotypes.
    Type: Application
    Filed: September 23, 2011
    Publication date: March 1, 2012
    Applicant: BASF Plant Science GmbH
    Inventors: Hee-Sook Song, Christian Dammann, Marc Morra, Jeffrey A. Brown, Liqun Xing, Hongmei Jia
  • Publication number: 20120046344
    Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Lipid transport and metabolism gene, in particular, by targeting natural antisense polynucleotides of a Lipid transport and metabolism gene. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of a Lipid transport and metabolism genes.
    Type: Application
    Filed: May 6, 2010
    Publication date: February 23, 2012
    Inventors: Joseph Collard, Olga Khorkova Sherman
  • Publication number: 20120046329
    Abstract: Disclosed herein are compositions and methods relating to modulators of Nod-like Receptors NOD1 (NLRC1) and NOD2 (NLRC2) signaling. Further provided are methods of identifying modulators of Nod-like Receptors NOD1 and NOD2 activity. Further provided are compositions and methods for treating or preventing inflammation, including diseases associated with inflammation such as inflammatory bowel diseases (Crohn's disease, ulcerative colitis), pancreatitis, arthritis, asthma, psoriasis. Alzheimer's disease, cardiovascular disease (arteritis), diabetes, and sepsis.
    Type: Application
    Filed: August 10, 2011
    Publication date: February 23, 2012
    Inventors: Gregory Paul Roth, Ricardo Garcia Correa, Pasha Moeenuddin Khan, John Christian Reed
  • Publication number: 20120040847
    Abstract: A program interface for diabetic users to streamline the process of carbohydrate counting of meals. The present invention helps diabetic patients keep track of their blood glucose levels and help the users to calculate their require insulin intake for each meal. The invention comprises of a database of foods which users can select from for the calculation of nutrition and carbohydrates. The users are able to select their assigned carbohydrate to insulin ratio for the calculation of the amount of insulin that is required for the meal. Essential data is then stored and accessible for future corrective analysis.
    Type: Application
    Filed: November 19, 2010
    Publication date: February 16, 2012
    Inventors: Mitchell Charles MANS, Lena Wilson Mans
  • Publication number: 20120039808
    Abstract: A promoter for differentiation of brain tumor initiating cells is provided.
    Type: Application
    Filed: August 11, 2011
    Publication date: February 16, 2012
    Applicant: The University of Tokyo
    Inventors: Kohei Miyazono, Hiroaki Ikushima, Keiji Miyazawa, Tomoki Todo, Yasushi Ino
  • Publication number: 20120015834
    Abstract: Methods and systems for determining a set of control molecules for use in a combinatorial approach for the treatment of medical conditions, including providing one or more sets of control molecules, where each control molecule within the set acts on a set of targets and the number of control molecules within the one or more sets of control molecules is fewer than the number of targets within the sets of targets; and searching within the sets of control molecules to identify a subset of control molecules that together with a subset of targets form an artificial system to produce a biological effect through the modulation of the subset of targets.
    Type: Application
    Filed: May 28, 2011
    Publication date: January 19, 2012
    Inventors: Giovanni Paternostro, Jacob D. Feala
  • Publication number: 20120004289
    Abstract: The instant invention provides methods and compositions for the diagnosis and treatment of cancer. The invention also provides method and compositions for determining if a subject is, or is at risk of becoming, chemoresistant.
    Type: Application
    Filed: March 5, 2010
    Publication date: January 5, 2012
    Applicant: The Johns Hopkins University
    Inventors: Jin Song, Zhen Zhang
  • Publication number: 20120004111
    Abstract: The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).
    Type: Application
    Filed: January 26, 2011
    Publication date: January 5, 2012
    Applicant: CosmosID Inc.
    Inventors: Rita R. COLWELL, Boyd Thomas LIVINGSTON, David JAKUPCIAK, Nur A. HASAN, John P. JAKUPCIAK, Douglas M. BRENNER
  • Publication number: 20110312510
    Abstract: The disclosure provides methods and kits for performing automated high-throughput assays to measure bactericidal activity in samples, such as plasma or sera from vaccinated subjects to evaluate the efficacy of vaccines against bacterial pathogens. The method combines obligatory linear-range data analysis, plate sealing and liquid volume handling for all assay steps to provide an automated, high-throughput measurement of bactericidal activity with favorable inter-assay and inter-operator variability.
    Type: Application
    Filed: June 16, 2010
    Publication date: December 22, 2011
    Inventors: Puiying Annie Mak, George Santos, Jeffrey Eugene Janes, John J. Donnelly, III
  • Publication number: 20110311511
    Abstract: The invention relates to the X-ray crystal structure of PfA-M1 aminopeptidase alone, and in complex with the phosphinate dipeptide analogue hPheP[CH2]Phe. More specifically the present invention provides the structure coordinates of PfA-M1 and PfA-M1 in complex with Co4. The invention also includes the use of the X-ray crystal structures as drug target models for anti-malarial drug design and a method for identifying or designing novel anti-malarial drugs, for example using high-throughput chemical screening and medicinal chemistry methods. The invention further provides anti-malarial drugs identified or designed according to the aforementioned method and their use for obstructing protein metabolism and synthesis in a parasite by blocking the entrance of Hb-derived peptides and/or blocking the exit of released amino acids at the active site of PfA-M1 protease.
    Type: Application
    Filed: February 12, 2009
    Publication date: December 22, 2011
    Inventors: James Charles Whisstock, Ashley Maurice Buckle, Sheena McGowan, Corrine Joy Porter, John P. Dalton, Jonathon Lowther, Colin Martin Stack, Sheila Mary Donnelly
  • Publication number: 20110312918
    Abstract: The present invention provides a novel mechanistic pathway and methods related to this pathway for the identification of compounds for the treatment of diseases involving cell proliferation, invasion and/or metastasis such as cancer. In particular, the instant invention relates to the phosphatase activity of Eya and the Eya-Six complex as a target for identifying novel therapeutic agents for the treatment of proliferative, invasive and/or metastatic disorders, and compositions identified using the methods disclosed herein.
    Type: Application
    Filed: December 8, 2009
    Publication date: December 22, 2011
    Applicant: Children's Hospital Medical Center
    Inventor: Rashmi Hegde