proteins

Summary

Summary: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

Top Publications

  1. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
  2. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
  3. doi The quest for orthologs: finding the corresponding gene across genomes
    Arnold Kuzniar
    Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
    Trends Genet 24:539-51. 2008
  4. pmc iRefIndex: a consolidated protein interaction database with provenance
    Sabry Razick
    The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
    BMC Bioinformatics 9:405. 2008
  5. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
  6. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
  7. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
  8. pmc CDD: a Conserved Domain Database for the functional annotation of proteins
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D225-9. 2011
  9. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
  10. ncbi Inference of macromolecular assemblies from crystalline state
    Evgeny Krissinel
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 372:774-97. 2007

Detail Information

Publications298 found, 100 shown here

  1. pmc ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    Markus Wiederstein
    Center of Applied Molecular Engineering, Division of Bioinformatics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
    Nucleic Acids Res 35:W407-10. 2007
    ..ProSA-web is accessible at https://prosa.services.came.sbg.ac.at...
  2. ncbi Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    Gerard Talavera
    Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
    Syst Biol 56:564-77. 2007
    ..This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies...
  3. doi The quest for orthologs: finding the corresponding gene across genomes
    Arnold Kuzniar
    Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
    Trends Genet 24:539-51. 2008
    ..Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a ..
  4. pmc iRefIndex: a consolidated protein interaction database with provenance
    Sabry Razick
    The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
    BMC Bioinformatics 9:405. 2008
    ..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...
  5. pmc PID: the Pathway Interaction Database
    Carl F Schaefer
    National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
    Nucleic Acids Res 37:D674-9. 2009
    ..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...
  6. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    ..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily...
  7. pmc KEGG: kyoto encyclopedia of genes and genomes
    M Kanehisa
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 28:27-30. 2000
    ..The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/)...
  8. pmc CDD: a Conserved Domain Database for the functional annotation of proteins
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D225-9. 2011
    ..Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of ..
  9. pmc The Protein Data Bank
    H M Berman
    Research Collaboratory for Structural Bioinformatics RCSB, Rutgers University, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 28:235-42. 2000
    ..This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource...
  10. ncbi Inference of macromolecular assemblies from crystalline state
    Evgeny Krissinel
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 372:774-97. 2007
    ..The method is implemented as a public WWW service...
  11. pmc InterPro: the integrative protein signature database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 37:D211-5. 2009
    ..data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files...
  12. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    ..BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome...
  13. pmc SIFT: Predicting amino acid changes that affect protein function
    Pauline C Ng
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N A1 162, Seattle, WA 98109, USA
    Nucleic Acids Res 31:3812-4. 2003
    ..We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html...
  14. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  15. pmc Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS
    Mariely DeJesus-Hernandez
    Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
    Neuron 72:245-56. 2011
    ..Our findings indicate that repeat expansion in C9ORF72 is a major cause of both FTD and ALS...
  16. ncbi MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    Jürgen Cox
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Biotechnol 26:1367-72. 2008
    ..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
  17. pmc Human non-synonymous SNPs: server and survey
    Vasily Ramensky
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 30:3894-900. 2002
    ..We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function ..
  18. pmc The RCSB Protein Data Bank: redesigned web site and web services
    Peter W Rose
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093 0743, USA
    Nucleic Acids Res 39:D392-401. 2011
    ..These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education...
  19. pmc The Amber biomolecular simulation programs
    David A Case
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Raod, TPC15, La Jolla, CA 92037, USA
    J Comput Chem 26:1668-88. 2005
    ..with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
  20. ncbi A statistical model for identifying proteins by tandem mass spectrometry
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:4646-58. 2003
    A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample...
  21. pmc NCBI Reference Sequences: current status, policy and new initiatives
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 4As 47B, 45 Center Drive, Bethesda, MD, USA
    Nucleic Acids Res 37:D32-6. 2009
    ..nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, ..
  22. doi Identification of host proteins required for HIV infection through a functional genomic screen
    Abraham L Brass
    Department of Genetics, Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Science 319:921-6. 2008
    HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs)...
  23. ncbi Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex
    D D Sarbassov
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 307:1098-101. 2005
    ..Rictor-mTOR may serve as a drug target in tumors that have lost the expression of PTEN, a tumor suppressor that opposes Akt/PKB activation...
  24. ncbi AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    R A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, UK
    J Biomol NMR 8:477-86. 1996
    ..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...
  25. pmc DrugBank: a knowledgebase for drugs, drug actions and drug targets
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 36:D901-6. 2008
    ..DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca...
  26. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Using html, the evidence for each prediction is shown in two ways: (i) a list of proteins of known localization with the most similar localization features to the query, and (ii) tables with detailed ..
  27. pmc Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus
    S Srinivas
    Department of Genetics and Development, Columbia University, New York, USA
    BMC Dev Biol 1:4. 2001
    ....
  28. ncbi Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    Richard A Friesner
    Department of Chemistry, Columbia University, New York, New York 10036, USA
    J Med Chem 47:1739-49. 2004
    ..Glide is also found to be more accurate than the recently described Surflex method...
  29. pmc MINT, the molecular interaction database: 2012 update
    Luana Licata
    Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    Nucleic Acids Res 40:D857-61. 2012
    ..bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction...
  30. pmc I-TASSER server for protein 3D structure prediction
    Yang Zhang
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA
    BMC Bioinformatics 9:40. 2008
    ..Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions...
  31. pmc InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
    Gabriel Ostlund
    Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
    Nucleic Acids Res 38:D196-203. 2010
    ..3 million proteins organized into 42.7 million pairwise ortholog groups...
  32. pmc Reactome knowledgebase of human biological pathways and processes
    Lisa Matthews
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 37:D619-22. 2009
    ..Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations...
  33. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale...
  34. ncbi In-gel digestion for mass spectrometric characterization of proteins and proteomes
    Andrej Shevchenko
    Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
    Nat Protoc 1:2856-60. 2006
    In-gel digestion of proteins isolated by gel electrophoresis is a cornerstone of mass spectrometry (MS)-driven proteomics. The 10-year-old recipe by Shevchenko et al. has been optimized to increase the speed and sensitivity of analysis...
  35. ncbi Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy
    Sophie Pattingre
    Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
    Cell 122:927-39. 2005
    ..Here, we show that wild-type Bcl-2 antiapoptotic proteins, but not Beclin 1 binding defective mutants of Bcl-2, inhibit Beclin 1-dependent autophagy in yeast and mammalian ..
  36. pmc The GOA database in 2009--an integrated Gene Ontology Annotation resource
    Daniel Barrell
    Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D396-403. 2009
    ..ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set...
  37. pmc STRING 8--a global view on proteins and their functional interactions in 630 organisms
    Lars J Jensen
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 37:D412-6. 2009
    Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation...
  38. ncbi The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
    Michael H Glickman
    Faculty of Biology and the Institute for Catalysis Science and Technology, Haifa, Israel
    Physiol Rev 82:373-428. 2002
    ..Although it was known that proteins do turn over, the large extent and high specificity of the process, whereby distinct proteins have half-lives ..
  39. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins...
  40. pmc An efficient algorithm for large-scale detection of protein families
    A J Enright
    Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK
    Nucleic Acids Res 30:1575-84. 2002
    ..family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or the presence of sequence motifs as well as ..
  41. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ..and demonstrate using a molecular-level evolutionary simulation, that selection against toxicity of misfolded proteins generated by ribosome errors suffices to create all of the observed covariation...
  42. ncbi Imaging intracellular fluorescent proteins at nanometer resolution
    Eric Betzig
    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Science 313:1642-5. 2006
    We introduce a method for optically imaging intracellular proteins at nanometer spatial resolution...
  43. pmc Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication
    Renate König
    Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 135:49-60. 2008
    Human Immunodeficiency Viruses (HIV-1 and HIV-2) rely upon host-encoded proteins to facilitate their replication...
  44. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
    ..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...
  45. ncbi UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
    ..Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences...
  46. pmc PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    Peter V Hornbeck
    Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA
    Nucleic Acids Res 40:D261-70. 2012
    ..resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1,30,000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and ..
  47. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
    We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP...
  48. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes...
  49. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ..This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates...
  50. ncbi Generalized lacZ expression with the ROSA26 Cre reporter strain
    P Soriano
    Nat Genet 21:70-1. 1999
  51. ncbi Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton
    D D Sarbassov
    Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Curr Biol 14:1296-302. 2004
    ..mTOR interacts with the raptor and GbetaL proteins to form a complex that is the target of rapamycin...
  52. pmc Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids
    Yasemin Sancak
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 141:290-303. 2010
    ..We show that amino acids induce the movement of mTORC1 to lysosomal membranes, where the Rag proteins reside...
  53. doi Drug target identification using side-effect similarity
    Monica Campillos
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 321:263-6. 2008
    ..Nine of these were tested and confirmed in cell assays, documenting the feasibility of using phenotypic information to infer molecular interactions and hinting at new uses of marketed drugs...
  54. doi Adapting proteostasis for disease intervention
    William E Balch
    Department of Cell Biology and Institute for Childhood and Neglected Diseases, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 319:916-9. 2008
    ....
  55. pmc AMPK phosphorylation of raptor mediates a metabolic checkpoint
    Dana M Gwinn
    Molecular and Cell Biology Laboratory, Dulbecco Center for Cancer Research, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Mol Cell 30:214-26. 2008
    ..These findings uncover a conserved effector of AMPK that mediates its role as a metabolic checkpoint coordinating cell growth with energy status...
  56. ncbi IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    Zsuzsanna Dosztanyi
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, PO Box 7, H 1518 Budapest, Hungary
    Bioinformatics 21:3433-4. 2005
    Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions...
  57. ncbi Protein folding and misfolding
    Christopher M Dobson
    University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
    Nature 426:884-90. 2003
    ..Folding and unfolding are crucial ways of regulating biological activity and targeting proteins to different cellular locations...
  58. pmc The IntAct molecular interaction database in 2010
    B Aranda
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D525-31. 2010
    ..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
  59. pmc ExoCarta 2012: database of exosomal proteins, RNA and lipids
    Suresh Mathivanan
    Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
    Nucleic Acids Res 40:D1241-4. 2012
    ..ExoCarta (http://www.exocarta.org) is a manually curated database of exosomal proteins, RNA and lipids. The database catalogs information from both published and unpublished exosomal studies...
  60. pmc Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications
    Sophie E Polo
    The Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB21QN, United Kingdom
    Genes Dev 25:409-33. 2011
    ..A common feature of DDR proteins is their mobilization in response to genotoxic stress...
  61. pmc iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, United States of America
    PLoS ONE 6:e18258. 2011
    Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e...
  62. pmc PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    Todd J Dolinsky
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Ave, Campus Box 8036, St Louis, MO 63110, USA
    Nucleic Acids Res 35:W522-5. 2007
    ..These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization...
  63. ncbi Locating proteins in the cell using TargetP, SignalP and related tools
    Olof Emanuelsson
    Stockholm Bioinformatics Center, AlbaNova, Stockholm University, SE 10691 Stockholm, Sweden
    Nat Protoc 2:953-71. 2007
    ..Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict ..
  64. doi Attributes of short linear motifs
    Norman E Davey
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Biosyst 8:268-81. 2012
    ..Enrichment for disorder in highly connected hub proteins and its correlation with organism complexity hint at the functional importance of disordered regions...
  65. ncbi Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    Yasushi Ishihama
    Laboratory of Seeds Finding Technology LSFT, Eisai Co, Ltd, 5 1 3 Tokodai, Tsukuba, Ibaraki 300 2635, Japan
    Mol Cell Proteomics 4:1265-72. 2005
    ..This was also the case for 46 proteins in a mouse whole cell lysate...
  66. ncbi Protein homology detection by HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, D 72076 Tubingen, Germany
    Bioinformatics 21:951-60. 2005
    ..Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction and evolution...
  67. pmc PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    Todd J Dolinsky
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA
    Nucleic Acids Res 32:W665-7. 2004
    ....
  68. pmc An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1
    Carson C Thoreen
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    J Biol Chem 284:8023-32. 2009
    ..Our findings challenge the assumption that rapamycin completely inhibits mTORC1 and indicate that direct inhibitors of mTORC1 kinase activity may be more successful than rapamycin at inhibiting tumors that depend on mTORC1...
  69. pmc Road to ruin: targeting proteins for degradation in the endoplasmic reticulum
    Melanie H Smith
    Department of Cellular and Molecular Pharmacology, Graduate Group in Biophysics and Howard Hughes Medical Institute, University of California San Francisco, CA 94158, USA
    Science 334:1086-90. 2011
    Some nascent proteins that fold within the endoplasmic reticulum (ER) never reach their native state...
  70. ncbi SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity
    Estela Jacinto
    Department of Physiology and Biophysics, UMDNJ Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
    Cell 127:125-37. 2006
    ..Our findings reveal that the SIN1-rictor-mTOR function in Akt-Ser473 phosphorylation is required for TORC2 function in cell survival but is dispensable for TORC1 function...
  71. pmc Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
    Joshua E Babiarz
    Institute for Regeneration Medicine, Center for Reproductive Sciences, University of California at San Francisco, San Francisco, California 94143, USA
    Genes Dev 22:2773-85. 2008
    ..Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes...
  72. pmc Infrastructure for the life sciences: design and implementation of the UniProt website
    Eric Jain
    Swiss Prot group, Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, 1211 Geneva 4, Switzerland
    BMC Bioinformatics 10:136. 2009
    ..Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008...
  73. ncbi Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Viktor Hornak
    Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794, USA
    Proteins 65:712-25. 2006
    ..It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems...
  74. pmc The role of dynamic conformational ensembles in biomolecular recognition
    David D Boehr
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
    Nat Chem Biol 5:789-96. 2009
    ....
  75. ncbi Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade
    P Li
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 75235, USA
    Cell 91:479-89. 1997
    ....
  76. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  77. pmc Data growth and its impact on the SCOP database: new developments
    Antonina Andreeva
    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK
    Nucleic Acids Res 36:D419-25. 2008
    The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships...
  78. ncbi HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    Cyril Dominguez
    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands
    J Am Chem Soc 125:1731-7. 2003
    ..In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 A backbone RMSD)...
  79. ncbi Substrate and functional diversity of lysine acetylation revealed by a proteomics survey
    Sung Chan Kim
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Mol Cell 23:607-18. 2006
    Acetylation of proteins on lysine residues is a dynamic posttranslational modification that is known to play a key role in regulating transcription and other DNA-dependent nuclear processes...
  80. pmc Associating genes and protein complexes with disease via network propagation
    Oron Vanunu
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000641. 2010
    ..complexes that are highly coherent in terms of the function, expression and conservation of their member proteins. Importantly, we apply our method to study three multi-factorial diseases for which some causal genes have been ..
  81. pmc The FoldX web server: an online force field
    Joost Schymkowitz
    Switch Laboratory, Flanders Interuniversity Institute for Biotechnology VIB, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
    Nucleic Acids Res 33:W382-8. 2005
    ..that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids...
  82. doi Atomic-level characterization of the structural dynamics of proteins
    David E Shaw
    D E Shaw Research, 120 West 45th Street, New York, NY 10036, USA
    Science 330:341-6. 2010
    ....
  83. ncbi PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
    Peter V Hornbeck
    Cell Signaling Technology, Beverly, MA 01915, USA
    Proteomics 4:1551-61. 2004
    ....
  84. pmc GENCODE: producing a reference annotation for ENCODE
    Jennifer Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 7:S4.1-9. 2006
    ..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
  85. ncbi Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    E Krissinel
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD, England
    Acta Crystallogr D Biol Crystallogr 60:2256-68. 2004
    ..A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign...
  86. pmc Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 5:e10972. 2010
    The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions...
  87. pmc The Database of Interacting Proteins: 2004 update
    Lukasz Salwinski
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, 90095 1570, USA
    Nucleic Acids Res 32:D449-51. 2004
    The Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) aims to integrate the diverse body of experimental evidence on protein-protein interactions into a single, easily accessible online database...
  88. pmc Extending CATH: increasing coverage of the protein structure universe and linking structure with function
    Alison L Cuff
    Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 39:D420-6. 2011
    ..1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of ..
  89. pmc STITCH 2: an interaction network database for small molecules and proteins
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 38:D552-6. 2010
    Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing...
  90. ncbi Development and testing of a general amber force field
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Comput Chem 25:1157-74. 2004
    ..GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, ..
  91. pmc BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
    Tiqing Liu
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D198-201. 2007
    ..The data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the Protein Data ..
  92. ncbi Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    Alexander D MacKerell
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
    J Comput Chem 25:1400-15. 2004
    Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem...
  93. pmc The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies
    Alison L Cuff
    Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
    Nucleic Acids Res 37:D310-4. 2009
    ..Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website...
  94. ncbi PRODRG: a tool for high-throughput crystallography of protein-ligand complexes
    Alexander W Schuttelkopf
    Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Scotland
    Acta Crystallogr D Biol Crystallogr 60:1355-63. 2004
    ..However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors...
  95. pmc The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1
    Yasemin Sancak
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology MIT, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 320:1496-501. 2008
    ..We find that the Rag proteins--a family of four related small guanosine triphosphatases (GTPases)--interact with mTORC1 in an amino acid-..
  96. doi Allosteric regulation and catalysis emerge via a common route
    Nina M Goodey
    Montclair State University, Department of Chemistry and Biochemistry, 1 Normal Avenue, Montclair, New Jersey 07043, USA
    Nat Chem Biol 4:474-82. 2008
    ..We summarize recent experimental data and the resulting insights into allostery within proteins, and we discuss the nature of future studies and the new applications that may result from increased ..
  97. ncbi A semiempirical free energy force field with charge-based desolvation
    Ruth Huey
    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92102, USA
    J Comput Chem 28:1145-52. 2007
    ..The force field shows improvement in redocking simulations over the previous AutoDock3 force field...
  98. pmc Global dynamics of proteins: bridging between structure and function
    Ivet Bahar
    Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
    Annu Rev Biophys 39:23-42. 2010
    ..With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence ..
  99. ncbi Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor
    A Brunet
    Children s Hospital and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cell 96:857-68. 1999
    ..In the presence of survival factors, Akt phosphorylates FKHRL1, leading to FKHRL1's association with 14-3-3 proteins and FKHRL1's retention in the cytoplasm...
  100. ncbi Quantitative mass spectrometry in proteomics: a critical review
    Marcus Bantscheff
    Cellzome AG, Meyerhofstrasse 1, 69254, Heidelberg, Germany
    Anal Bioanal Chem 389:1017-31. 2007
    ..These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic ..
  101. pmc PepX: a structural database of non-redundant protein-peptide complexes
    Peter Vanhee
    VIB Switch Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
    Nucleic Acids Res 38:D545-51. 2010
    ..Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database...

Research Grants164 found, 100 shown here

  1. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2013
    ..It contains B27PD, a small protein fragment, which is similar to proteins in the parts of the eye being attacked by the immune system...
  2. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2012
    ..It contains B27PD, a small protein fragment, which is similar to proteins in the parts of the eye being attacked by the immune system...
  3. Understanding/ Treating Neuropsychiatric Symptoms of Pediatric Physical Illness
    Eva Szigethy; Fiscal Year: 2009
    ..abstract_text> ..
  4. Bioengineering Core for Cellular and Tissue Models
    Andrew McCulloch; Fiscal Year: 2009
    ..uses flat silicone rubber membranes, onto which stripes are deposited that consist of extra-cellular matrix proteins to guide cell attachment (Gopalan et al., 2003). This technique is shown in Fig...
  5. Discovery metabolite profiling of the prolyl peptidases
    Alan Saghatelian; Fiscal Year: 2009
    ..Researchers have recently developed a number of methods to identify the genes, proteins, and metabolites associated with disease...
  6. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  7. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  8. National Biomedical EPR Center
    James Hyde; Fiscal Year: 2003
    ..labeling (SDSL) is a rapidly growing field with many applications to structure and dynamics of nucleic acids and proteins. The use of this method for membrane proteins is of fundamental significance because, in many cases, SDSL is the ..
  9. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  10. Biomedical Simulations Resource (BMSR)
    DAVID Z D apos ARGENIO; Fiscal Year: 2010
    ..2005 Pioneer Application --- 2 vitro selections against multiple proteins. The work creates enormous, unexplored opportunities in chemical evolution...
  11. NIH Director's Pioneer Award
    Junying Yuan; Fiscal Year: 2009
    ..No Abstract provided ..
  12. A Network Biology Approach to Antibiotic Action and Bacterial Defense Mechanisms
    James Collins; Fiscal Year: 2009
    ..there is a need for systems biology and synthetic biology approaches to discern the interplay between genes, proteins and pathways in furthering our understanding of how bacteria respond and defend themselves against antibiotics...
  13. Understanding the Cognitive Impact of Early Life Epilepsy
    Frances Jensen; Fiscal Year: 2009
    ..Finally, we will determine whether similar alterations in signaling, regulatory, and synaptic proteins also are observed in human tissue following seizures and in cases of autism associated with neonatal or infantile ..
  14. Project 1: In vitro Studies: Correlate the physical and chemical characteristics
    David L Eaton; Fiscal Year: 2011
    ..and human macrophage-like cells, and that short-term exposure is associated with changes in the expression of proteins and cellular factors that are biomarkers of oxidative stress...
  15. Biomedical Simulations Resource (BMSR)
    DAVID D ARGENIO; Fiscal Year: 2009
    ..2005 Pioneer Application --- 2 vitro selections against multiple proteins. The work creates enormous, unexplored opportunities in chemical evolution...
  16. 2007 NIH Director's Pioneer Award Program (DP1)
    Rustem Ismagilov; Fiscal Year: 2009
    ..These two technologies will be used together to understand protein aggregation and aging, and may lead to new hypothesis and molecules for controlling these processes. ..
  17. Chymase-Mediated MMP Activation in Ishemia Reperfusion Injury
    LOUIS DELL ITALIA; Fiscal Year: 2009
    ..I) to Ang II (11,12), mast cell chymase activates interstitial MMPs (13-18) and directly degrades cell surface proteins such as fibronectin (19), resulting in smooth muscle cell (20,21) and cardiomyocyte (22) death...
  18. Chymase-Mediated MMP Activation in Ishemia Reperfusion Injury
    LOUIS JOSEPH DELL'ITALIA; Fiscal Year: 2013
    ..I) to Ang II (11,12), mast cell chymase activates interstitial MMPs (13-18) and directly degrades cell surface proteins such as fibronectin (19), resulting in smooth muscle cell (20,21) and cardiomyocyte (22) death...
  19. Tissue Culture Laboratory
    Joseph Goldstein; Fiscal Year: 2009
    ..by Protein G chromatography of more than 20 different polyclonal rabbit antibodies directed against the multiple proteins that are studied in this Program Project Grant...
  20. Molecular Biology Core Laboratory
    David Russell; Fiscal Year: 2009
    ..This Core laboratory provides support for acrylamide gel electrophoresis of proteins, DMA sequencing, analysis of gene expression by oligonucleotide microarray hybridization and real-time polymerase ..
  21. ADMINISTRATIVE CORE
    Dennis L Kasper; Fiscal Year: 2011
    ..Biomolecule Production Core has assisted investigators with the production of over 100 different recombinant proteins and carbohydrate preparations;this core has conducted nearly 300 fermentations, resulting in 44 kg of bacterial ..
  22. DCTD Biopharmaceutical Development
    LARRY ARTHUR; Fiscal Year: 2009
    ..leading-edge technologies for development of monoclonal antibodies, cytokines, immunotoxins and other recombinant proteins, peptide and DNA vaccines, virus vaccines and targeted cytolytic viruses, gene therapy products, and other ..
  23. DCTD Biopharmaceutical Development - Type 1 Diabetes RAID projects
    LARRY ARTHUR; Fiscal Year: 2009
    ..leading-edge technologies for development of monoclonal antibodies, cytokines, immunotoxins and other recombinant proteins, peptide and DNA vaccines, virus vaccines and targeted cytolytic viruses, gene therapy products, and other ..
  24. DCTD Biopharmaceutical Development
    David Heimbrook; Fiscal Year: 2012
    ..leading-edge technologies for development of monoclonal antibodies, cytokines, immunotoxins and other recombinant proteins, peptide and DNA vaccines, virus vaccines and targeted cytolytic viruses, gene therapy products, and other ..
  25. DCTD Biopharmaceutical Development
    David Heimbrook; Fiscal Year: 2011
    ..leading-edge technologies for development of monoclonal antibodies, cytokines, immunotoxins and other recombinant proteins, peptide and DNA vaccines, virus vaccines and targeted cytolytic viruses, gene therapy products, and other ..
  26. DCTD Biopharmaceutical Development
    LARRY ARTHUR; Fiscal Year: 2010
    ..leading-edge technologies for development of monoclonal antibodies, cytokines, immunotoxins and other recombinant proteins, peptide and DNA vaccines, virus vaccines and targeted cytolytic viruses, gene therapy products, and other ..
  27. DCTD Biopharmaceutical Development
    David Heimbrook; Fiscal Year: 2013
    ..leading-edge technologies for development of monoclonal antibodies, cytokines, immunotoxins and other recombinant proteins, peptide and DNA vaccines, virus vaccines and targeted cytolytic viruses, gene therapy products, and other ..
  28. Mice Humanized with Hepatocytes and iPS Cells from Patients with Metabolic Diseas
    Stephen C Strom; Fiscal Year: 2010
    ..performs over 3,000 functions critical to maintaining the organism, ranging from production and secretion of proteins such as albumin, clotting factors and antiproteases, to metabolism and excretion of exogenous compounds such as ..
  29. Mice Humanized with Hepatocytes and iPS Cells from Patients with Metabolic Diseas
    Stephen Strom; Fiscal Year: 2009
    ..performs over 3,000 functions critical to maintaining the organism, ranging from production and secretion of proteins such as albumin, clotting factors and antiproteases, to metabolism and excretion of exogenous compounds such as ..
  30. Optimization of DNA Repair by Abh8
    Lauren Endres; Fiscal Year: 2013
    ..The DDR is a broad cellular response involving a network of proteins that are highly conserved between yeast and mammals [4]...
  31. DCTD Human Toxicology and Pharmacology
    LARRY ARTHUR; Fiscal Year: 2010
    ..technology platforms, such as nanodispersions and emulsions, targeted nano-particles, and targeted carrier proteins. Although not all NCEs will have been formulatable by the end of the second step, this strategy is expected to ..
  32. DCTD Human Toxicology and Pharmacology
    David Heimbrook; Fiscal Year: 2012
    ..technology platforms, such as nanodispersions and emulsions, targeted nano-particles, and targeted carrier proteins. Although not all NCEs will have been formulatable by the end of the second step, this strategy is expected to ..
  33. DCTD Human Toxicology and Pharmacology
    David Heimbrook; Fiscal Year: 2011
    ..technology platforms, such as nanodispersions and emulsions, targeted nano-particles, and targeted carrier proteins. Although not all NCEs will have been formulatable by the end of the second step, this strategy is expected to ..
  34. DCTD Human Toxicology and Pharmacology
    LARRY ARTHUR; Fiscal Year: 2009
    ..technology platforms, such as nanodispersions and emulsions, targeted nano-particles, and targeted carrier proteins. Although not all NCEs will have been formulatable by the end of the second step, this strategy is expected to ..
  35. DCTD Human Toxicology and Pharmacology
    David Heimbrook; Fiscal Year: 2013
    ..technology platforms, such as nanodispersions and emulsions, targeted nano-particles, and targeted carrier proteins. Although not all NCEs will have been formulatable by the end of the second step, this strategy is expected to ..
  36. CFI Pathogen Inactivation Technology
    Trevor P Castor; Fiscal Year: 2010
    ..and pathogenic bacteria;(3) evaluate the potential of applying SFS-CFI enabling technology to human plasma proteins such as fibrinogen and other components;and (4) evaluate compatibility of SFS-CFI with other enabling pathogen ..
  37. CFI Pathogen Inactivation Technology
    TREVOR CASTOR; Fiscal Year: 2009
    ..and pathogenic bacteria;(3) evaluate the potential of applying SFS-CFI enabling technology to human plasma proteins such as fibrinogen and other components;and (4) evaluate compatibility of SFS-CFI with other enabling pathogen ..
  38. Probing the Structure of the Synapse Using Superresolution Light Microscopy
    Gina Turrigiano; Fiscal Year: 2009
    ..approaches have begun to piece together how interactions between neurotransmitter receptors and other synaptic proteins regulate and control synaptic strength and plasticity, but a major limitation is that there is little or no ..
  39. Mapping for Specialized Domains for FCeRI Signaling &Internalization
    Bridget S Wilson; Fiscal Year: 2013
    ..Based upon recent evidence, we propose that membrane proteins are concentrated in "protein islands," protein and cholesterol-rich domains separated by expanses of mostly lipid...
  40. Iron in the pathogenesis of Friedreich's ataxia
    ARNULF HANS WERNER KOEPPEN; Fiscal Year: 2010
    ..failing iron homeostasis can still be assessed by the "downstream" effects of iron on iron-responsive proteins among which ferritin, mitochondrial ferritin, and ferroportin are most likely to undergo changes...
  41. Vaccine Development for Falciparum Malaria in Pregnant Women and Their Offspring
    Ian C Michelow; Fiscal Year: 2013
    ..Candidate vaccine proteins will be screened, confirmed and selected for clinical trials using pioneering molecular tools and blood samples ..
  42. NITRIC OXIDE SYNTHASE IN THE JUXTAGLOMERULAR APPARATUS
    Christopher S Wilcox; Fiscal Year: 2010
    ..SHR, by the addition of drugs to the perfusates, or use of small interference RNAs targeting NHERF-2 or specific proteins involved in production, metabolism and transport of ADMA and ROS and in vascular function in mice transgenic for ..
  43. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia J Savin; Fiscal Year: 2010
    ..The molecular basis for recurrent FSGS is unknown although abnormal podocyte proteins associated with familial FSGS have been identified...
  44. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia J Savin; Fiscal Year: 2009
    ..The molecular basis for recurrent FSGS is unknown although abnormal podocyte proteins associated with familial FSGS have been identified...
  45. ROLE OF S-ADENOSYLMETHIONINE ON UBC9 AND SUMOYLATION IN LIVER CANCER AND ALCOHOLI
    Maria Lauda Tomasi; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Posttranslational modifications mediated by ubiquitin-like proteins regulate a variety of cellular pathways...
  46. Hypothalamic Orexin Role in Menopause-Associated Hot Flashes and Mood/Sleep Disru
    PHILIP LEE JOHNSON; Fiscal Year: 2013
    ..tracing compounds, and ex vivo functional brain imaging using immunohistochemistry to detect immediate early gene proteins. In 2008 and 2010, I was respectively promoted to Research Assistant Professor, and then to Assistant Professor ..
  47. PROJECT 1: ROTH: Functionally Selective Antagonists and Engineered Receptors
    Bryan Roth; Fiscal Year: 2009
    ..Many proteins are involved in the post-endocytic decision-making process including GASP, SNX-1 and ubiquitin ligases...
  48. H1R Signaling and Immune Deviation in EAE
    Cory Teuscher; Fiscal Year: 2013
    ..Since we found no difference in G-protein activation of allelic H1R-Ga fusion proteins, this suggested that H1R signaling may also involve a novel non-G-protein b-arrestin pathway...
  49. H1R Signaling and Immune Deviation in EAE
    Cory Teuscher; Fiscal Year: 2010
    ..Since we found no difference in G-protein activation of allelic H1R-Ga fusion proteins, this suggested that H1R signaling may also involve a novel non-G-protein b-arrestin pathway...
  50. Cross-talk Between Coagulation, Inflammation, and Immunity
    Lawrence L Leung; Fiscal Year: 2013
    ..thrombomodulin and in that context, thrombin's function is "modulated'and will activate two other proteins, protein C and procarboxypeptidase B (pCPB)...
  51. Phosphorylation of FGF23 coordinates crosstalk between the skeleton and kidney
    VINCENT SCOTT TAGLIABRACCI; Fiscal Year: 2013
    ..The majority of phosphoproteins are intracellular;however, numerous extracellular proteins are also phosphorylated...
  52. Regulation of ER stress-induced cell death
    Randal J Kaufman; Fiscal Year: 2013
    ..that islets from Chop-/- mice are protected from oxidative stress that occurs upon accumulation of unfolded proteins in the ER...
  53. STRUCTURE, BIOSYNTHESIS AND FUNCTION OF GLYCOPROTEINS
    Stuart Kornfeld; Fiscal Year: 2007
    ..GST peptides with these amino acids will be used to isolate proteins that recognize these motifs...
  54. Mitochondrial Dysfunction and Adipose Insulin Resistance
    David A Bernlohr; Fiscal Year: 2013
    ..proteomic, metabolomic and molecular analyses that point toward the covalent modification of mitochondrial proteins with bioactive lipids and the oxidation of mitochondrial thioredoxin as central to the process...
  55. Role of JAK2-PAK1 interaction in prolactin-dependent signaling
    Maria Diakonova; Fiscal Year: 2013
    ..Tyrosine (Tyr) kinase JAK2 was identified as a PRLR-bound signaling molecule. Identification of the proteins recruited to the PRLR-JAK2 and dissection of the signaling pathways that are subsequently activated will ..
  56. Structural and molecular basis of drug-induced IKACh reduction
    SAMI FOUAD NOUJAIM; Fiscal Year: 2012
    ..I elucidated the roles of sarcolemmal inward rectifier (Kir2.x) potassium channel proteins in the maintenance of VF, and of the ryanodine receptor type 2 in the initiation of ventricular tachyarrhythmias ..
  57. Structural and molecular basis of drug-induced IKACh reduction
    SAMI FOUAD NOUJAIM; Fiscal Year: 2013
    ..I elucidated the roles of sarcolemmal inward rectifier (Kir2.x) potassium channel proteins in the maintenance of VF, and of the ryanodine receptor type 2 in the initiation of ventricular tachyarrhythmias ..
  58. Molecular Mechanisms of Parvovirus Gene Expression and Replication
    Jianming Qiu; Fiscal Year: 2013
    ..of B19V mRNAs, and generates abundant small viral mRNAs for encoding two small non- structural viral proteins, i.e. 7.5-kDa and 11-kDa...
  59. MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SA
    Buddy Ullman; Fiscal Year: 2003
    ..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
  60. MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SA
    Buddy Ullman; Fiscal Year: 2001
    ..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
  61. MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SA
    Buddy Ullman; Fiscal Year: 2000
    ..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
  62. MECHANISM BASED DRUG SELECTION AND DESIGN--NUCLEOTIDE SA
    Buddy Ullman; Fiscal Year: 1999
    ..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
  63. MECHANISM-BASED DRUG SELECTION AND DESIGN: NUCLEOTIDE SA
    Buddy Ullman; Fiscal Year: 2002
    ..These reagents are expected to permit structure-based discovery of new drug classes that target proteins necessary for parasite survival...
  64. Metabolic mechanisms of antiestrogen resistance in breast cancer
    UBALDO EMILIO MARTINEZ OUTSCHOORN; Fiscal Year: 2013
    ..I will stain a human tumor microarray (TMA) of patients with ER+ breast cancer treated with tamoxifen for the proteins listed in aim 1...
  65. Analysis of gene regulation of Vibrio cholerae during infection
    Jun Zhu; Fiscal Year: 2013
    ..cholerae proteins and other pathogens. We will first investigate how V...
  66. Role of Peroxidasin in Glomerular Matrix Homeostasis
    Gautam Bhave; Fiscal Year: 2013
    ..HOX are highly reactive and oxidatively halogenate proteins to adversely affect cell function...
  67. Lipid Droplet Metabolism
    Fredric B Kraemer; Fiscal Year: 2013
    ..physical properties of LDs are distinctively altered in quantifiably defined ways by specific droplet-associated proteins and these physical properties contribute to LD size (growth and fusion) and metabolism...
  68. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Identification of Proteins Important for Male Osteoporosis Osteoporosis is a major public health problem, mainly characterized by low bone mineral density (BMD)...
  69. Molecular Mechanisms of Disease Progression in Myeloid Malignancy
    ELIZABETH ANN EKLUND; Fiscal Year: 2013
    ..Stat3, Stat5 and Xiap proteins are also increased in Icsbp-/- cells in a Gas2/calpain-dependent manner...
  70. MECHANISMS OF RADIORESISTANCE AND CELL CYCLE PROGRESSION
    Howard B Lieberman; Fiscal Year: 2013
    ..metastasis, including migration towards fibronectin, invasion, cell adhesion to various extracellular matrix proteins, and metastatic behavior in an in vivo model...
  71. Modifiers of Cyst Progression in Polycystic Kidney Disease
    Phillip Darwin Bell; Fiscal Year: 2013
    ..by applicant): Polycystic kidney disease (PKD) is a "ciliopathic" disease since the loss of cilia or mutations in proteins involved in the function of cilia lead to renal cystic development...
  72. A Novel Thioredoxin Mimetic Prodrug for Prevention of Bronchopulmonary Dysplasia
    Prakash Jagtap; Fiscal Year: 2013
    ..Compounding this increase in superoxide production is the developmental deficiency of anti-oxidant proteins, such as superoxide dismutase and Trx, that are present in insufficient quantity at an early gestational age...
  73. Growth Hormone Regulation of SH2B1
    Christin Carter-Su; Fiscal Year: 2013
    ..ligands, and to gain insight into unrecognized cellular actions of GH;new functions of SH2B1;and how scaffold proteins such as SH2B1 move highly regulated and dynamic complexes from membrane-bound receptors to multiple, often remote,..
  74. High throughput screen for selective inhibitors of cyclophilin B
    Richard J Bram; Fiscal Year: 2013
    ..improved therapies will be accelerated by the identification of compounds that specifically target novel cellular proteins that contribute to tumr cell survival...
  75. RSK-2 regulates integrin-mediated adhesion and migration
    JOE WILLIAM RAMOS; Fiscal Year: 2013
    ..We have found that the proteins PEA-15 and RSK2 may conspire to influence cell adhesion and migration...
  76. Mechanistic Studies on Prostate Cancer Prevention by Gugulipid
    Dong Xiao; Fiscal Year: 2013
    ..treated with vehicle (control) and GL for assay of apoptosis and levels of apoptosis and autophagy regulating proteins. Innovation and Significance: We trust that our proposal falls under the criteria of innovative research because ..
  77. Role of Membrane Modifications in the Bioactivities of Conjugated Linoleic Acids
    Papasani V Subbaiah; Fiscal Year: 2013
    ..The effect of CLA on the distribution of raft-associated proteins will be investigated in cultured cells, as well as in primary adipocytes and hepatocytes from mice and rats...
  78. The PKCepsilon-regulated oncogenic and tumor suppressor roles of ATF2 in melanoma
    ERIC KIRK LAU; Fiscal Year: 2013
    ..In Aim 2, I propose to determine how specifically ATF2 activates Bcl2 proteins and modulates HK1:VDAC1 complexes to promote mitochondrial membrane leakage...
  79. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia Savin; Fiscal Year: 2009
    ..The molecular basis for recurrent FSGS is unknown although abnormal podocyte proteins associated with familial FSGS have been identified...
  80. Role of poly (ADP-ribose) polymerase 1 (PARP-1) in experimental colitis
    Claire Larmonier; Fiscal Year: 2013
    ..PARPs) constitute a family of 18 cell signaling enzymes, which are involved in the regulation of DNA-binding proteins and DNA repair...
  81. Hepatitis B virus replication and DDB1
    Betty L Slagle; Fiscal Year: 2013
    ..Additionally, MS data will be mined for evidence that HBV replication induces recruitment of immune regulatory proteins to the Cul4-DDB1 complex...
  82. Mindfulness Based Stress Reduction as an Adjunctive Treatment for Psoriasis
    Jan A Moynihan; Fiscal Year: 2013
    ..Cytokines (small molecular weight messenger proteins) produced by T helper (Th)1 and Th17 lymphocytes, antigen presenting cells, and leukocytes have been implicated ..
  83. Suppression of Ocular Scarring - Controlled Delivery of an ALK-5 Inhibitor
    Hiroshi Nakamura; Fiscal Year: 2013
    ..In our previous experiments, the ALK-5 inhibitor SB-505124 induced a marked reduction in downstream proteins of TGF-2 in vitro...
  84. Integrating stress MAP kinase signaling with DNA replication origin licensing
    Jeanette Gowen Cook; Fiscal Year: 2013
    ..Our long-term goal is to determine precisely how origin licensing proteins are regulated by intracellular cell cycle cues and by extracellular signaling pathways...
  85. Role of Vimentin in Pathogenesis of CNS Inflammation
    Sheng He Huang; Fiscal Year: 2013
    ..Vim has emerged as an organizer of a number of critical proteins involved in cell adhesion/migration and cell signaling...
  86. Targeting GRK2 (BARK1) in Heart Failure
    Walter J Koch; Fiscal Year: 2012
    ..evidence that a large and dynamic "GRK2 interactome" exists in cells and extends GRK2 activity and regulation to proteins outside of GPCRs...
  87. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..that EBNA1 functions at the viral origin of plasmid DNA replication (OriP) through interactions with several host proteins important for chromosome integrity, including telomere repeat binding factors (TRFs), DNA replication pausing ..
  88. The role of LKB1 in the maintenance of genomic stability.
    Zhi Xiang Xu; Fiscal Year: 2013
    ..We found that LKB1 interacts with ATM, BRCA1, and other DNA damage response (DDR) proteins in vivo...
  89. Identifying underlying mechanisms of intracellular changes in response to caregiv
    MELANIE SARAH FLINT; Fiscal Year: 2013
    ..extensive proteomic profiling revealed that stress can trigger significant changes in several actin regulating proteins important for T cell cytoskeletal rearrangement and cell migration in rodents...