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

Publications297 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. doi 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.
  16. 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 ..
  17. 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.
  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. 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...
  20. 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, ..
  21. 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)...
  22. 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...
  23. 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...
  24. 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...
  25. 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 ..
  26. 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...
  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. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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 ..
  35. 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...
  36. 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...
  37. 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...
  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. 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...
  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. 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...
  42. 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...
  43. 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...
  44. 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 ..
  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. 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...
  47. 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...
  48. 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...
  49. ncbi Generalized lacZ expression with the ROSA26 Cre reporter strain
    P Soriano
    Nat Genet 21:70-1. 1999
  50. 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...
  51. 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...
  52. 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...
  53. 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
    ....
  54. 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...
  55. 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...
  56. 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...
  57. 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...
  58. 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...
  59. 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...
  60. 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...
  61. 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...
  62. 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 ..
  63. 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...
  64. 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...
  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. 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
    ....
  67. 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...
  68. 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...
  69. 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...
  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 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...
  72. 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...
  73. 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
    ....
  74. 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
    ....
  75. 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...
  76. 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...
  77. 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)...
  78. 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...
  79. 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 ..
  80. 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...
  81. 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
    ....
  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. 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...
  84. 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...
  85. 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...
  86. 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...
  87. 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 ..
  88. 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...
  89. 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, ..
  90. 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 ..
  91. 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...
  92. 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...
  93. 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...
  94. 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-..
  95. 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...
  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. 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 ..
  98. pmc Benchmarking sets for molecular docking
    Niu Huang
    Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Building, 1700 4th Street, Box 2550, San Francisco, California 94143 2550, USA
    J Med Chem 49:6789-801. 2006
    ..DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/...
  99. 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...
  100. 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...
  101. 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 ..

Research Grants80

  1. 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...
  2. 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...
  3. Apoptosis and Trophoblast Fusion
    Neal Rote; Fiscal Year: 2009
    ..phospholipids to form a phosphatidylserine (PS)-rich exofacial surface, expression and insertion of fusion proteins into the plasma membrane, and rearrangement of actin cytoskeletal elements...
  4. Apoptosis and Trophoblast Fusion
    NEAL STEWART ROTE; Fiscal Year: 2010
    ..phospholipids to form a phosphatidylserine (PS)-rich exofacial surface, expression and insertion of fusion proteins into the plasma membrane, and rearrangement of actin cytoskeletal elements...
  5. ADIPOCYTE PROTEIN SECRETION AND INSULIN ACTION
    Harvey Lodish; Fiscal Year: 2007
    ..endo-/exocytotic compartments in 3T3-L1 adipocytes including vesicles which transport membrane associated proteins like GLUT4, secreted proteins where secretion is stimulated by insulin such as ARCP30 (adipocyte complement ..
  6. Ty3 viruslike particle morphogenesis and host interactions
    Suzanne Sandmeyer; Fiscal Year: 2010
    ..terminal repeat retrotransposon in budding yeast containing GAG3 and POL3 ORFs encoding structural and catalytic proteins, respectively...
  7. A novel transgenic silkworm system for recombinant glycoprotein production
    Donald Jarvis; Fiscal Year: 2009
    Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
  8. A novel transgenic silkworm system for recombinant glycoprotein production
    Donald L Jarvis; Fiscal Year: 2010
    Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
  9. A novel transgenic silkworm system for recombinant glycoprotein production
    Donald Jarvis; Fiscal Year: 2007
    Many biomedically significant proteins, including antibodies, cytokines, anticoagulants, blood clotting factors, and others are glycoproteins...
  10. CHEMISTRY AND BIOLOGY OF PLATINUM ANTICANCER DRUGS
    STEPHEN LIPPARD; Fiscal Year: 2007
    ..Working against this process is nucleotide excision repair (NER) of the adducts. The binding of cellular proteins, such as HMGB1, to DNA across from cisplatin cross-links shields them from NER and sensitizes cells to the drug...
  11. CELL CYCLE REGULATION OF THE YEAST HO GENE
    LINDA BREEDEN; Fiscal Year: 2001
    ..Most of the research proposal is an investigation of the proteins and protein binding sites required for these two waves of transcriptional activation...
  12. NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINS
    Frances Walker; Fiscal Year: 2009
    ..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas' disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...
  13. NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINS
    Frances Walker; Fiscal Year: 2009
    ..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas' disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...
  14. Brucella epitope recognition by CD8+ T cells
    Gary Splitter; Fiscal Year: 2009
    Brucella melitensis, an intracellular human pathogen, is largely controlled by CD8+ T cells, but the Brucella proteins containing peptides recognized by protective CD8+ T cells remain unknown...
  15. Brucella epitope recognition by CD8+ T cells
    JEROME SCOTT HARMS; Fiscal Year: 2010
    Brucella melitensis, an intracellular human pathogen, is largely controlled by CD8+ T cells, but the Brucella proteins containing peptides recognized by protective CD8+ T cells remain unknown...
  16. Genetic control of limb development by Pbx
    Licia Selleri; Fiscal Year: 2010
    ..biochemical analyses, for the last fifteen years the prevailing view has been that Pbx/Exd primarily helps Hox proteins execute their developmental programs. Hence, Pbx proteins have been named as "Hox cofactors"...
  17. NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINS
    Frances Walker; Fiscal Year: 2006
    We have discovered a series of heme proteins in the saliva of the blood-sucking bug Rhodnius prolixus that act as vasodilators, anti-platelet aggregation and anti-histaminic agents when injected into the victim...
  18. NITRIC OXIDE INTERACTION WITH INSECT NITROPHORINS
    FRANCES ANN WALKER; Fiscal Year: 2010
    ..basin, which carries the parasite Trypanasoma cruzi, the vector of Chagas'disease, contains a suite of heme proteins that we have named Nitrophorins (NPs)...
  19. Vaccinia Virus Genetics and Morphogenesis
    Richard C Condit; Fiscal Year: 2010
    ..The core contains the viral DNA and at least 50 viral proteins. Core substructures can be distinguished by electron microscopy, including lateral bodies, a core wall, and a ..
  20. Investigation of protein interactions in intrinsic blood coagulation pathway
    Divi Venkateswarlu; Fiscal Year: 2007
    ..During the requested funding period, we propose to develop structural assembly of multi-domain proteins associated with intrinsic blood coagulation pathway...