protein databases

Summary

Summary: DATABASES containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.

Top Publications

  1. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
  2. 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
  3. 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
  4. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
  5. ncbi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    Joshua E Elias
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Methods 4:207-14. 2007
  6. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
  7. 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
  8. 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
  9. pmc TM-align: a protein structure alignment algorithm based on the TM-score
    Yang Zhang
    Center of Excellence in Bioinformatics, University at Buffalo 901 Washington Street, Buffalo, NY 14203, USA
    Nucleic Acids Res 33:2302-9. 2005
  10. pmc ExPASy: The proteomics server for in-depth protein knowledge and analysis
    Elisabeth Gasteiger
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:3784-8. 2003

Detail Information

Publications261 found, 100 shown here

  1. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
  2. 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
    ..InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/)...
  3. 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
    ..The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins...
  4. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred...
  5. ncbi Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    Joshua E Elias
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Methods 4:207-14. 2007
    ....
  6. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
    ..GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script...
  7. 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...
  8. 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...
  9. pmc TM-align: a protein structure alignment algorithm based on the TM-score
    Yang Zhang
    Center of Excellence in Bioinformatics, University at Buffalo 901 Washington Street, Buffalo, NY 14203, USA
    Nucleic Acids Res 33:2302-9. 2005
    ..This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align...
  10. pmc ExPASy: The proteomics server for in-depth protein knowledge and analysis
    Elisabeth Gasteiger
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 31:3784-8. 2003
    ..ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community...
  11. ncbi Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    J Gough
    Laboratory of Molecular Biology, MRC, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 313:903-19. 2001
    ..The annotations derived from these matches are available from a public web server at: http://stash.mrc-lmb.cam.ac.uk/SUPERFAMILY. This server also enables users to match their own sequences against the SUPERFAMILY model library...
  12. ncbi TANDEM: matching proteins with tandem mass spectra
    Robertson Craig
    Manitoba Centre for Proteomics, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
    Bioinformatics 20:1466-7. 2004
    ..AVAILABILITY: The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors...
  13. ncbi Scoring function for automated assessment of protein structure template quality
    Yang Zhang
    Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
    Proteins 57:702-10. 2004
    ..These data suggest that the TM-score is a useful complement to the fully automated assessment of protein structure predictions. The executable program of TM-score is freely downloadable at http://bioinformatics.buffalo.edu/TM-score...
  14. 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
    ..Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. STRING can be reached at http://string-db.org/...
  15. pmc Protein database searches using compositionally adjusted substitution matrices
    Stephen F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEBS J 272:5101-9. 2005
    ..In a typical database search, at least one of these criteria is satisfied by over half the related sequence pairs. Compositional substitution matrix adjustment is now available in NCBI's protein-protein version of blast...
  16. ncbi Open mass spectrometry search algorithm
    Lewis Y Geer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Proteome Res 3:958-64. 2004
    ..At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets...
  17. ncbi Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    Alasdair T R Laurie
    School of Biochemistry and Microbiology, University of Leeds, UK
    Bioinformatics 21:1908-16. 2005
    ..Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster...
  18. 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 in BindingDB are linked both to structural data in the PDB via PDB IDs and chemical and sequence searches, and to the literature in PubMed via PubMed IDs...
  19. ncbi The DISOPRED server for the prediction of protein disorder
    Jonathan J Ward
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    Bioinformatics 20:2138-9. 2004
    ..AVAILABILITY: The server can be accessed by non-commercial users at http://bioinf.cs.ucl.ac.uk/disopred/..
  20. ncbi ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    Fabian Glaser
    The George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Bioinformatics 19:163-4. 2003
    ..We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins...
  21. pmc The TIGRFAMs database of protein families
    Daniel H Haft
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:371-3. 2003
    ..The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs...
  22. ncbi A human protein atlas for normal and cancer tissues based on antibody proteomics
    Mathias Uhlen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    Mol Cell Proteomics 4:1920-32. 2005
    ..Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research...
  23. pmc PDBsum new things
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D355-9. 2009
    ..Furthermore, it now accepts users' own PDB format files and generates a private set of analyses for each uploaded structure...
  24. ncbi The CCPN data model for NMR spectroscopy: development of a software pipeline
    Wim F Vranken
    Macromolecular Structure Database, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    Proteins 59:687-96. 2005
    ..The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research...
  25. ncbi Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    Hon Nian Chua
    Graduate School for Integrated Sciences and Engineering, National University of Singapore, Singapore
    Bioinformatics 22:1623-30. 2006
    ..We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction...
  26. 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
    ..SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop...
  27. pmc SUBA: the Arabidopsis Subcellular Database
    Joshua L Heazlewood
    ARC Centre of Excellence in Plant Energy Biology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia 35 Stirling Highway, Crawley 6009, Western Australia, Australia
    Nucleic Acids Res 35:D213-8. 2007
    ..The SUBA database provides a powerful means by which to assess protein subcellular localisation in Arabidopsis (http://www.suba.bcs.uwa.edu.au)...
  28. 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
    ..Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function...
  29. ncbi The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    Zsuzsanna Dosztanyi
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518 Budapest, PO Box 7, Hungary
    J Mol Biol 347:827-39. 2005
    ..This application we term IUPred and compare its performance with three generally accepted predictors, PONDR VL3H, DISOPRED2 and GlobPlot on a database of disordered proteins...
  30. pmc DisProt: the Database of Disordered Proteins
    Megan Sickmeier
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Nucleic Acids Res 35:D786-93. 2007
    ..In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at http://www.disprot.org...
  31. pmc The importance of intrinsic disorder for protein phosphorylation
    Lilia M Iakoucheva
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Nucleic Acids Res 32:1037-49. 2004
    ....
  32. ncbi Advances and pitfalls of protein structural alignment
    Hitomi Hasegawa
    Institute of Biotechnology, University of Helsinki, P O Box 56 Viikinkaari 5, 00014 University of Helsinki, Finland
    Curr Opin Struct Biol 19:341-8. 2009
    ..Advances have been made in algorithmic robustness, multiple alignment, and speeding up database searches...
  33. pmc UniProt: the Universal Protein knowledgebase
    Rolf Apweiler
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D115-9. 2004
    ..The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt...
  34. ncbi OPM: orientations of proteins in membranes database
    Mikhail A Lomize
    College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109 1065, USA
    Bioinformatics 22:623-5. 2006
    ..All coordinate files with the calculated membrane boundaries are available for downloading...
  35. pmc HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
    Tania Lima
    Swiss Prot group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 37:D471-8. 2009
    ..Thanks to the implementation of HAMAP, more than 200,000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: http://www.expasy.org/sprot/hamap)...
  36. pmc LGA: A method for finding 3D similarities in protein structures
    Adam Zemla
    Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
    Nucleic Acids Res 31:3370-4. 2003
    ..LGA also allows the clustering of similar fragments of protein structures...
  37. pmc InterProScan: protein domains identifier
    E Quevillon
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W116-20. 2005
    ..O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results...
  38. pmc STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
    Matthias Heinig
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
    Nucleic Acids Res 32:W500-2. 2004
    ..A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/...
  39. ncbi Prediction of protein subcellular localization
    Chin Sheng Yu
    Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
    Proteins 64:643-51. 2006
    ..Furthermore, we also develop a practical hybrid method, which combines the two-level SVM classifier and the homology search method, as a general tool for the sequence annotation of subcellular localization...
  40. pmc SMART 6: recent updates and new developments
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 37:D229-32. 2009
    ..In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service...
  41. pmc TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
    Jeremy D Selengut
    TIGR, Bioinformatics Department, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 35:D260-4. 2007
    ..The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties...
  42. pmc NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 6An 12J, 45 Center Drive, Bethesda, MD 20892 6510, USA
    Nucleic Acids Res 35:D61-5. 2007
    ..The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence...
  43. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D138-41. 2004
    ..Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/)...
  44. ncbi The HMMTOP transmembrane topology prediction server
    G E Tusnády
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary
    Bioinformatics 17:849-50. 2001
    ..This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments...
  45. 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
    ..Reactome's data content and software can all be freely used and redistributed under open source terms...
  46. pmc PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    EMBO Rep 9:429-34. 2008
    ..Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics...
  47. pmc PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
    Florian Gnad
    Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 8:R250. 2007
    ..For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites...
  48. ncbi Design of a novel globular protein fold with atomic-level accuracy
    Brian Kuhlman
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Science 302:1364-8. 2003
    ..2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature...
  49. pmc STRING: a database of predicted functional associations between proteins
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:258-61. 2003
    ..The database predicts functional interactions at an expected level of accuracy of at least 80% for more than half of the genes; it is online at http://www.bork.embl-heidelberg.de/STRING/...
  50. pmc Enzyme-specific profiles for genome annotation: PRIAM
    Clotilde Claudel-Renard
    Laboratoire de Genetique Cellulaire, INRA, INRA CNRS, BP27, 31326 Castanet Tolosan Cedex, France
    Nucleic Acids Res 31:6633-9. 2003
    ..The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes...
  51. ncbi Protein function prediction--the power of multiplicity
    Robert Rentzsch
    Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
    Trends Biotechnol 27:210-9. 2009
    ..On the downside, multiplicity is often confusing. We therefore systematically review methods and resources for automated protein function prediction, looking at individual (biochemical) and contextual (network) functions, respectively...
  52. pmc Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    John C Obenauer
    Center for Cancer Research, E18 580, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Nucleic Acids Res 31:3635-41. 2003
    ..In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu...
  53. ncbi Exploring the functional landscape of gene expression: directed search of large microarray compendia
    Matthew A Hibbs
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    Bioinformatics 23:2692-9. 2007
    ..This vast repository is still underutilized due to the lack of methods for fast, accurate exploration of the entire compendium...
  54. ncbi InterProScan--an integration platform for the signature-recognition methods in InterPro
    E M Zdobnov
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 17:847-8. 2001
    ..InterProScan is designed to be a scalable and extensible system with a robust internal architecture...
  55. ncbi Recent progress in protein subcellular location prediction
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Anal Biochem 370:1-16. 2007
  56. ncbi Template-based modeling and free modeling by I-TASSER in CASP7
    Yang Zhang
    Center for Bioinformatics, Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
    Proteins 69:108-17. 2007
    ..Especially, there is no high-resolution model below 2 A for the FM targets. These problems highlight the issues that need to be addressed in the next generation of atomic-level I-TASSER development especially for the FM target modeling...
  57. pmc OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
    Feng Chen
    Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Nucleic Acids Res 34:D363-8. 2006
    ..OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species, and will be updated and expanded as additional genome sequence data become available...
  58. 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...
  59. pmc Prediction of protein binding regions in disordered proteins
    Bálint Mészáros
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
    PLoS Comput Biol 5:e1000376. 2009
    ..Through its generality, ANCHOR opens new ways to study the essential functional sites of disordered proteins...
  60. pmc ARAMEMNON, a novel database for Arabidopsis integral membrane proteins
    Rainer Schwacke
    Universitat zu Koln, Botanisches Institut, Gyrhofstrasse 15, 50931 Koln, Germany
    Plant Physiol 131:16-26. 2003
    ..and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de...
  61. pmc PrDOS: prediction of disordered protein regions from amino acid sequence
    Takashi Ishida
    Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 35:W460-4. 2007
    ..The prediction results are sent by e-mail, and the server also provides a web-interface to check the results...
  62. ncbi Ligand Depot: a data warehouse for ligands bound to macromolecules
    Zukang Feng
    Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA
    Bioinformatics 20:2153-5. 2004
    ..rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux...
  63. 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...
  64. ncbi Interpretation of shotgun proteomic data: the protein inference problem
    Alexey I Nesvizhskii
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 4:1419-40. 2005
    ....
  65. 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
    ....
  66. ncbi Functional and topological characterization of protein interaction networks
    Soon Hyung Yook
    Department of Physics, University of Notre Dame, Notre Dame, IN 46556, USA
    Proteomics 4:928-42. 2004
    ....
  67. ncbi Preformed structural elements feature in partner recognition by intrinsically unstructured proteins
    Monika Fuxreiter
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
    J Mol Biol 338:1015-26. 2004
    ..This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner...
  68. pmc DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    Ioannis Xenarios
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, PO Box 951570, UCLA, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 30:303-5. 2002
    ..Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database...
  69. pmc APD: the Antimicrobial Peptide Database
    Zhe Wang
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198 6805, USA
    Nucleic Acids Res 32:D590-2. 2004
    ..APD is a useful tool for studying the structure-function relationship of antimicrobial peptides. The database can be accessed via a web-based browser at the URL: http://aps.unmc.edu/AP/main.html...
  70. ncbi Open source system for analyzing, validating, and storing protein identification data
    Robertson Craig
    Beavis Informatics Ltd, and Manitoba Center for Proteomics, Winnipeg, Manitoba, Canada
    J Proteome Res 3:1234-42. 2004
    ..The components of the system have been made available as open source development projects. A publicly available system has been established, comprised of a group of data analysis servers and one main database server...
  71. 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...
  72. pmc The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
    Jun Adachi
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz, D 82152 Martinsried, Germany
    Genome Biol 7:R80. 2006
    ..Here we applied these methods to the analysis of the human urinary proteome...
  73. pmc MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    Sitao Wu
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, Kansas 66047, USA
    Proteins 72:547-56. 2008
    ..0 x 10(-13), which demonstrates the effect of additional structural information on the protein fold recognition. The MUSTER server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/MUSTER...
  74. ncbi Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
    Karin Julenius
    Center for Biological Sequence Analysis, BioCentrum, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Glycobiology 15:153-64. 2005
    ..NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc...
  75. ncbi Protein-protein docking with backbone flexibility
    Chu Wang
    Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    J Mol Biol 373:503-19. 2007
    ..The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models...
  76. ncbi Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA
    J Proteome Res 5:1888-97. 2006
    ..A web server, called "Euk-OET-PLoc", has been designed at http://202.120.37.186/bioinf/euk-oet for public to predict subcellular locations of eukaryotic proteins by the fusion OET-KNN classifier...
  77. pmc The PeptideAtlas project
    Frank Desiere
    Institute for Systems Biology, Seattle, WA, USA
    Nucleic Acids Res 34:D655-8. 2006
    ..Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds...
  78. pmc Assembly reflects evolution of protein complexes
    Emmanuel D Levy
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nature 453:1262-5. 2008
    ..Our model of self-assembly allows reliable prediction of evolution and assembly of a complex solely from its crystal structure...
  79. pmc Metrics for GO based protein semantic similarity: a systematic evaluation
    Catia Pesquita
    XLDB, Departamento de Informatica, Faculdade de Ciencias da Universidade de Lisboa, Campo Grande Edifício C6, Lisboa, Portugal
    BMC Bioinformatics 9:S4. 2008
    ..Another issue, is whether electronic annotations should or not be used in semantic similarity calculations...
  80. ncbi Rotamer libraries in the 21st century
    Roland L Dunbrack
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia PA 19111, USA
    Curr Opin Struct Biol 12:431-40. 2002
    ....
  81. ncbi The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    Renxiao Wang
    Department of Internal Medicine and Comprehensive Cancer Center, University of Michigan Medical School, 1500 E Medical Center Drive, Ann Arbor, MI 48109 0934, USA
    J Med Chem 47:2977-80. 2004
    ..The outcomes of this project have been organized into a Web-accessible database named the PDBbind database...
  82. ncbi PISCES: a protein sequence culling server
    Guoli Wang
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 19:1589-91. 2003
    ..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output...
  83. ncbi The human plasma proteome: a nonredundant list developed by combination of four separate sources
    N Leigh Anderson
    The Plasma Proteome Institute, Washington DC 20009 3450, USA
    Mol Cell Proteomics 3:311-26. 2004
    ..The resulting nonredundant list confirms the presence of a number of interesting candidate marker proteins in plasma and serum...
  84. pmc Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave, Menlo Park CA 94025, USA
    Nucleic Acids Res 34:W645-50. 2006
    ..All three web services are available at http://www.pantherdb.org/tools...
  85. pmc The Transporter Classification Database: recent advances
    Milton H Saier
    Division of Biological Sciences and Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Nucleic Acids Res 37:D274-8. 2009
    ..The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users...
  86. ncbi ConFunc--functional annotation in the twilight zone
    Mark N Wass
    Structural Bioinformatics Group, Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    Bioinformatics 24:798-806. 2008
    ..This combination of steps produces a set of feature (GO annotation) derived profiles from which protein function is predicted...
  87. ncbi RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
    Aart J Nederveen
    Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
    Proteins 59:662-72. 2005
    ..The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord...
  88. 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
    ..This core functionality will be further extended as more FoldX applications are developed...
  89. ncbi Relating protein pharmacology by ligand chemistry
    Michael J Keiser
    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco California 94143 2550, USA
    Nat Biotechnol 25:197-206. 2007
    ..These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves...
  90. pmc ProbCons: Probabilistic consistency-based multiple sequence alignment
    Chuong B Do
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 15:330-40. 2005
    ..On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource...
  91. 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...
  92. ncbi Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics
    Christoph Steinbeck
    Cologne University Bioinformatics Center CUBIC, Germany
    Curr Pharm Des 12:2111-20. 2006
    ..This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software...
  93. pmc AAindex: amino acid index database, progress report 2008
    Shuichi Kawashima
    Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai Minato ku Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D202-5. 2008
    ..The database can be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.jp/dbget-bin/www_bfind?aaindex) or downloaded by anonymous FTP (ftp://ftp.genome.jp/pub/db/community/aaindex/)...
  94. pmc MODBASE, a database of annotated comparative protein structure models and associated resources
    Ursula Pieper
    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
    Nucleic Acids Res 37:D347-54. 2009
    ..MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)...
  95. pmc 3did Update: domain-domain and peptide-mediated interactions of known 3D structure
    Amelie Stein
    Institute for Research in Biomedicine, Barcelona Supercomputing Center, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
    Nucleic Acids Res 37:D300-4. 2009
    ..A web-based tool to query 3did is available at http://3did.irbbarcelona.org...
  96. ncbi Progress and challenges in predicting protein-protein interaction sites
    Iakes Ezkurdia
    Centro Nacional de Biotechnolgia, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Brief Bioinform 10:233-46. 2009
    ..We provide suggestions for effective feature selection, and make it clear that community standards for testing, training and performance measures are necessary for progress in the field...
  97. pmc The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools
    John Klimek
    Institute for Systems Biology, Seattle, Washington 98103, USA
    J Proteome Res 7:96-103. 2008
    ..All data, including the native raw instrument and mzXML formats and the PeptideProphet validated peptide assignments, are available at http://regis-web.systemsbiology.net/PublicDatasets/...
  98. pmc CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    Joe Dundas
    Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
    Nucleic Acids Res 34:W116-8. 2006
    ..The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins...
  99. ncbi Transmembrane proteins in the Protein Data Bank: identification and classification
    Gabor E Tusnady
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary
    Bioinformatics 20:2964-72. 2004
    ....
  100. pmc SuperPose: a simple server for sophisticated structural superposition
    Rajarshi Maiti
    Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Nucleic Acids Res 32:W590-4. 2004
    ..The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/...
  101. ncbi MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
    W Hayes McDonald
    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
    Rapid Commun Mass Spectrom 18:2162-8. 2004
    ....

Research Grants63

  1. Discovery of a urine biomarker of HIV for noninvasive, point-of-care testing use
    Hans P Schlecht; Fiscal Year: 2011
    ..To discover such a biomarker(s), we will use LC-MS/MS and human/HIV protein databases to identify urinary proteins/protein degradation products in subjects with highly active HIV replication...
  2. Center for Computational Mass-Spectrometry
    Pavel A Pevzner; Fiscal Year: 2011
    ..four directions: (i) enabling complex mass spectrometry searches, (ii) analyzing unknown proteomes without protein databases, (iii) analyzing altered proteomes, and (iv) constructing proteogenomic annotations and analyzing pathways...
  3. The development of tools for proteomic analysis in trypanosomes
    Michael P Rout; Fiscal Year: 2012
    ..With the wealth of information available from genome sequences and protein databases, we believe the methods we seek to develop will be a useful addition not only to proteomic studies in ..
  4. Center for Computational Mass-Spectrometry
    Pavel A Pevzner; Fiscal Year: 2013
    ..four directions: (i) enabling complex mass spectrometry searches, (ii) analyzing unknown proteomes without protein databases, (iii) analyzing altered proteomes, and (iv) constructing proteogenomic annotations and analyzing pathways...
  5. DEVELOPMENT OF A PRIMATE GENOMIC RESOURCE
    Michael G Katze; Fiscal Year: 2012
    ..shotgun proteomics and Fourier transform ion cyclotron resonance mass spectrometry to build macaque specific protein databases for use in identifying proteins present in various rhesus macaque tissues...
  6. Automated Integration of Biomedical Knowledge
    Gil Alterovitz; Fiscal Year: 2010
    ..we have successfully applied it to the analysis and engineering of Gene Ontology, the development gene and protein databases, and the identification of peripheral biomarkers of disease progression and drug response...
  7. Protein function prediction by statistical phylogenomics
    Steven E Brenner; Fiscal Year: 2010
    ..We will collaborate with major protein databases to deploy SIFTER for medium-scale application in protein annotation...
  8. Searching Environmental Metagenomes for Novel Infectious Cancer Agents (PQ12)
    James M Pipas; Fiscal Year: 2013
    ..causing agents are then identified among these nonhuman sequences by searching public nucleic acid and protein databases and identifying similar sequences that can then be associated with a known virus, bacteria or other organism...
  9. Automated High-Throuput Estimation and Modeling of Protein Network Distributions
    GUSTAVO KUNDE ROHDE; Fiscal Year: 2013
    ..to be microtubule-associated will be tested for selected examples by comparison with information in existing protein databases and literature and by additional experimentation...
  10. Towards the Building of a Comprehensive Searchable Biological Experiment Database
    Hong Yu; Fiscal Year: 2009
    ..Those algorithms and tools will enhance bioscience information retrieval, information extraction, summarization, and question answering. ..
  11. Building and Validating Location Proteomics Databases
    Robert F Murphy; Fiscal Year: 2011
    ..The determined location for each protein will be compared to whatever information is available from protein databases, journal articles and location predictors...
  12. A Core Database of Interacting Proteins
    Lukasz Salwinski; Fiscal Year: 2013
    ..DIP is a free and open community resource for research physicians and scientists. DIP takes special care in documenting the accuracy of the data it contains. ..
  13. COMPUTER STUDIES OF PROTEIN STRUCTURE AND FUNCTION
    Barry H Honig; Fiscal Year: 2013
    ..more protein sequences than protein structures so it is necessary to find ways to amplify the information in protein databases if structure is to be fully integrated in genome scale research...
  14. 2007 Electron Distribution & Chemical Bonding Gordon Research Conference
    Carlo Gatti; Fiscal Year: 2007
    ..Charge density protein databases will be discusses as a way to extend the experimental CD methodology to biocrystallography...
  15. Automated Literature Mining for Validation of High-Throughput Function Prediction
    KARIN MARIA VERSPOOR; Fiscal Year: 2010
    ..from full text journal publications;(3) high-throughput text mining;and (4) using primary information in protein databases to evaluate the methods...
  16. TRANSCRIPTIONAL CONTROL OF DEVELOPING CILIARY EPITHELIUM
    Elena Frolova; Fiscal Year: 2004
    ..Finally, mouse and human homologs of the ciliary epithelium-specific transcription factors will be obtained by searching DNA and protein databases and their relevance to human hereditary eye diseases will be evaluated.
  17. MULTIPLE REPRESENTATIONS OF BIOLOGICAL SEQUENCES
    Douglas Brutlag; Fiscal Year: 1999
    ..using test sets and crossvalidation methods, 3) compare these networks with other methods for searching protein databases , 4) build an integrated set of Bayesian networks to predict protein secondary structure, 5) compare the ..
  18. Surface Shape Based Screening of Large Protein Databases
    Daisuke Kihara; Fiscal Year: 2009
    ..The docking algorithm will be applied to protein-protein interaction data of coli. ..
  19. Chemical Genetic Approach to Melanocyte Chemosensitivity
    Seth Orlow; Fiscal Year: 2004
    ..Microsequencing of affinity-isolated targets will be performed and used to identify targets from protein databases. Findings from the proposed studies will result in a deeper understanding of the cellular pathways ..
  20. ASYMMETRICALLY EXPRESSED GENES IN DEVELOPING CEREBRUM
    Daniel Geschwind; Fiscal Year: 2003
    ..novel genes, about 25 percent of which have no EST (expressed sequence tag) matches in the nucleic acid and protein databases. This and other data suggest that the utility of further microarray screening of this RDA is far from ..
  21. LIPID Metabolites And Pathways Strategy (LIPID MAPS)
    Eoin Fahy; Fiscal Year: 2013
    ..and academic sectors by actively maintaining and updating the lipid structure and lipid-related gene/protein databases, by maintaining all integrated biochemical and signaling pathways on the website, by continuing to host all ..
  22. Cloning and analysis of centrosome-associated RNA
    MARK ALLIEGRO; Fiscal Year: 2007
    ..determine if cRNAs encode proteins, identify functional domains, and discover homologues in nucleic acid and protein databases. We will determine if they are closely associated with the centrosome in vitro and in situ...
  23. ACQUISITION OF A MASS SPECTROMETRY RESOURCE
    Jeffery Kelly; Fiscal Year: 2000
    ..The SEQUEST software package will be obtained to analyze protein mass spectrometric data and search the protein databases. This equipment will allow separation of proteins and peptides by HPLC, direct analysis of their molecular ..
  24. Diabetes Mellitus:Molecular Signaling,Genes/Therapeutics
    Michael Czech; Fiscal Year: 2004
    ..will also explore the integration and utility of information derived from recently obtained gene and protein databases, as well as repositories of protein-protein interactions...
  25. Database for Glycan Structures
    Ram Sasisekharan; Fiscal Year: 2005
    ..This forms the framework for the present STTR grant application as a fast-track Phases I and II grant application that is highly integrated towards addressing the requirements of the glycomics field. ..
  26. Proteomic Pathways for Pancreatic Cancer Stem Cells
    David Lubman; Fiscal Year: 2009
    ..be further fractionated using nonporous RP-HPLC and identified based upon LC-MS/MS of the peptides against protein databases where we expect to identify around 2500 proteins...
  27. Axima-CFR MALDI TOF Mass Spectrometer
    EDWARD FEENER; Fiscal Year: 2003
    Recent advances in protein sequence analysis by mass spectroscopy combined with the availability of large protein databases have created unique opportunities in diabetes research...
  28. DIFFERENTIAL PROTEIN EXPRESSION BY MALDI TOF MS
    David Lubman; Fiscal Year: 2002
    ..and peptide maps can be used to identify each protein and search for modification of proteins compared to protein databases. Capillary Electrophoresis/Electrospray Ionization Tandem Mass Spectrometry (CE(ESI)-TOFMS-MS) will be used ..
  29. Identification of The Membranous Nephropathy Antigen
    David Salant; Fiscal Year: 2005
    ..Peptide sequences will be used to search protein databases to identify known proteins, search EST databases for matching cDNA clones, or to design oligonucleotides to ..
  30. Computer cluster for computational biology
    Ron Elber; Fiscal Year: 2005
    ..The combined unification of optimal hardware and software for computational biology and bioinformatic will make the new cluster; an outstanding resource for NIH related research ..
  31. DIHYDRONEOPTERIN ALDOLASE, A TUBERCULOSIS DRUG TARGET
    WILLIAM SULING; Fiscal Year: 2002
    ..It will also provide purified DHNA for future drug discovery studies based upon structure-activity relationships, molecular modeling and crystallographic structure-based drug design. ..
  32. Multidimensional Protein Identification
    Bruce Torbett; Fiscal Year: 2006
    ..infrastructure designed to facilitate data analysis, management, archiving, and links to public protein databases. The establishment of a TSRI institutional Proteomics Core would provide resources whereby all TSRI ..
  33. ACT Database: Protein Structure-Function Relationships
    JAMES BOWIE; Fiscal Year: 2005
    ..Linking ACT more closely to other databases, such as the Database of Interacting Proteins (DIP), based here at UCLA. ..
  34. Genome-wide Cardiac Transciption Patterns post-MI
    Richard McCormick; Fiscal Year: 2003
    ..For ESTs, a combination of standard clustering algorithms and domain/motif searches of protein databases will be used to generate patterns, classifications, and possible functional annotations...
  35. DNA SEQUENCE CORE FACILITY
    MARK MCINTOSH; Fiscal Year: 1990
    ..in automated nucleotide sequencing and immediate information access to sequence analysis software and DNA/protein databases. To achieve this objective, we are requesting capital funds to purchase an integrated instrumentation/..
  36. Purchase of a Linear Ion Trap/Fourier Transform Mass Spectrometer
    Robert Cotter; Fiscal Year: 2007
    ..Many of the studies here are proteomics studies, utilizing protein databases for identification of proteins in complex mixtures (as well as their PTMs) from their digested peptides...
  37. Diabetes Mellitus and the Control of Energy Metabolism
    Silvia Corvera; Fiscal Year: 2005
    ..The meeting will seek to integrate this information with gene and protein databases from humans and model systems such as rodents, yeast, drosophila and C.elegans...
  38. PROTEIN SEQUENCE AND ANNOTATION SEARCH SYSTEM
    Hongzhan Huang; Fiscal Year: 2000
    ..The annotation search will utilize information available from protein databases, such as keywords and taxonomy...
  39. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005
    ..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
  40. Combined Methods for Protein-Structure Prediction
    Kevin Karplus; Fiscal Year: 2007
    ....
  41. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong Li; Fiscal Year: 2010
    ..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
  42. SIMULATION OF PROTEIN UNFOLDING AND FOLDING
    Michael Levitt; Fiscal Year: 2001
    ....
  43. FUNCTION DIVERGENCE IN PROTEIN FAMILIES
    Adam Godzik; Fiscal Year: 2003
    ..With the flood of new sequences coming from large scale genome sequencing projects, it is identifying the possible function of these proteins that would make these data so important. ..
  44. ATP-DEPENDENT PROTEIN KINASES IN GRAM-POSITIVE BACTERIA
    Milton Saier; Fiscal Year: 2004
    ..abstract_text> ..
  45. Detecting relations among heterogeneous genomic datasets
    William Noble; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  46. ESCHERICHIA COLI INVASION OF BRAIN ENDOTHELIAL CELLS
    Sheng He Huang; Fiscal Year: 2007
    ..To further characterize the role of IbeABP in E. coil K1 invasion of human BMEC. (3). To determine how E. coil K1 invasion gene expression is regulated by the IbeR and environmental signals (glucose and oxygen tension). ..
  47. Machine learning analysis of tandem mass spectra
    William Stafford Noble; Fiscal Year: 2010
    ....
  48. From Genomic Sequences to Protein Structure and Function
    John Moult; Fiscal Year: 2007
    ..Proteins for study will be chosen on the basis of three considerations: likely impact of the splice forms on protein structure, functional role of the splicing, and relevance to disease. ..
  49. High-Accuracy Models of Proteins from Remote Homology
    Jie Liang; Fiscal Year: 2009
    ..These computational capabilities could have profound impacts to drug design and disease studies. ..
  50. Q-TOF Hybrid Quadrupole/Orthogonal TOF Mass Spectrometer
    Dominic Desiderio; Fiscal Year: 2004
    ..Clearly, a state-of-the-art MALDI-based mass spectrometer with MS/MS capabilities is needed to support the rapidly increasing number of extensive and diverse research programs on the UTHSC campus. ..
  51. ROBUST PORTABLE SOFTWARE FOR LOCATION PROTEOMICS
    Robert Murphy; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  52. Mapping worm fat gene networks
    ALBERTHA WALHOUT; Fiscal Year: 2006
    ..In addition, we recently developed a version of the yeast one-hybrid system that enables us to map fat TF-fat gene interactions in a high-throughput manner. ..
  53. Conformational linkage during catalysis by TrpRS
    Charles Carter; Fiscal Year: 2005
    ..Ground-state destabilization in TrpRS likely has close analogies with similar phenomena in such enzymes. ..
  54. EVOLUTION OF IMMUNE RECOGNITION AND EVASION
    Austin L Hughes; Fiscal Year: 2010
    ..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
  55. Integrated state-of-the-art LC-MS/NMR system for the University of Wisconsin
    John Markley; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  56. Technologies Trageting Mitochondral Proteome
    BRIAN BALGLEY; Fiscal Year: 2005
    ..abstract_text> ..
  57. GENOMIC ENZYMOLOGY: THE ENOLASE SUPERFAMILY
    JOHN GERLT; Fiscal Year: 2006
    ..4) We will test a structural blueprint for functional diversity in the (beta/alpha)7beta-barrel fold by determining whether new functions can be generated by in vitro evolution. ..
  58. Bioinformatics linkage of protein disorder and function
    A Dunker; Fiscal Year: 2006
    ..previous research, so the first aims will be to enlarge and exhaustively annotate our ordered and disordered protein databases. Using the annotated data, we propose next to compare different bioinformatics and datamining strategies to ..
  59. A Computational Genotyping System for Improved Influenza Surveillance
    Guoqing Lu; Fiscal Year: 2010
    ..With the genotyping database system, newly emerging influenza A viral genotypes can be identified in a timely and cost-effective manner. ..
  60. PHOSPHATE TRANSPORT PATHS WITHIN HOMODIMERIC PTP
    Hartmut Wohlrab; Fiscal Year: 2001
    ..The structure will permit the accurate localization of the functionally relevant residues and regions of PTP and should lead to a good understanding of transmembrane metabolite transport. ..
  61. Modeling of Protein Interactions 2007
    Sandor Vajda; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable] [unreadable]..