protein sequence analysis

Summary

Summary: A process that includes the determination of an amino acid sequence of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.

Top Publications

  1. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
  2. 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
  3. ncbi Clustal W and Clustal X version 2.0
    M A Larkin
    The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 23:2947-8. 2007
  4. 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
  5. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
  6. 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
  7. 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
  8. 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
  9. pmc Multiple sequence alignment with the Clustal series of programs
    Ramu Chenna
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3497-500. 2003
  10. pmc SWISS-MODEL: An automated protein homology-modeling server
    Torsten Schwede
    Biozentrum der Universitat Basel, Klingelbergstr 50 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 31:3381-5. 2003

Research Grants

  1. NON-GASTRIN ACID SECRETAGOGUE IN ISLET CELL TUMORS
    William Chey; Fiscal Year: 1990
  2. ALDEHYDE DEHYDROGENASE AND PATHOGENESIS OF ALCOHOLISM
    REGINA PIETRUSZKO; Fiscal Year: 1993
  3. DIABETES MELLITUS & ISLET AMYLOID POLYPEPTIDE (IAAP)
    Kenneth Johnson; Fiscal Year: 1991
  4. Signal Transduction Mechanisms in Ocular Albinism
    Vinit Mahajan; Fiscal Year: 2005
  5. ROLE OF AEROMONAS HYDROPHILA VIRULENCE FACTORS
    CLIFFORD HOUSTON; Fiscal Year: 1992
  6. DOXORUBICIN BIOSYNTHESIS AND RESISTANCE
    CHARLES SIH; Fiscal Year: 2000
  7. ROLE OF THYROGLOBULIN IN THYROXINE BIOSYNTHESIS
    ALLEN RAWITCH; Fiscal Year: 1990
  8. CA2+ RELEASE CHANNEL FROM CARDIAC SARCOPLASMIC RETICULUM
    Kevin Campbell; Fiscal Year: 1991
  9. REGULATION OF TRACHEA MUCIN SYNTHESIS AND GLYCOSYLATION
    Joseph Mendicino; Fiscal Year: 1990
  10. CLONING OF THE HUMAN RECEPTOR FOR ALPHA-2-INTERFERON
    LINVILLE MEADOWS; Fiscal Year: 1990

Detail Information

Publications281 found, 100 shown here

  1. pmc MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Robert C Edgar
    Nucleic Acids Res 32:1792-7. 2004
    ..The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle...
  2. 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...
  3. ncbi Clustal W and Clustal X version 2.0
    M A Larkin
    The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 23:2947-8. 2007
    ..ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/..
  4. 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...
  5. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
    ..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment...
  6. 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...
  7. 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...
  8. 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
    ..Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains...
  9. pmc Multiple sequence alignment with the Clustal series of programs
    Ramu Chenna
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3497-500. 2003
    ..Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/)...
  10. pmc SWISS-MODEL: An automated protein homology-modeling server
    Torsten Schwede
    Biozentrum der Universitat Basel, Klingelbergstr 50 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 31:3381-5. 2003
    ..The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server...
  11. 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
    ....
  12. ncbi HyPhy: hypothesis testing using phylogenies
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego San Diego, CA 92103, USA
    Bioinformatics 21:676-9. 2005
    ..AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org...
  13. 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...
  14. 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...
  15. ncbi ESyPred3D: Prediction of proteins 3D structures
    Christophe Lambert
    Facultes Universitaires Notre Dame de la Paix, Unité de Recherche en Biologie Moléculaire, rue de Bruxelles, 61, B 5000 Namur, Belgium
    Bioinformatics 18:1250-6. 2002
    ..The target-template alignment step is generally accepted as the most critical step in homology modeling...
  16. pmc PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    Mikita Suyama
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 34:W609-12. 2006
    ..Another distinct feature is that the user can specify a subregion of the input alignment in order to specifically analyze functional domains or exons of interest. The PAL2NAL server is available at http://www.bork.embl.de/pal2nal...
  17. 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...
  18. 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/..
  19. ncbi Boosting classifier for predicting protein domain structural class
    Kai Yan Feng
    Imaging Science and Biomedical Engineering, Medical School, The University of Manchester, Manchester, M13 9PT, UK
    Biochem Biophys Res Commun 334:213-7. 2005
    ..It is anticipated that LogitBoost can also become a useful vehicle in classifying other attributes of proteins according to their sequences, such as subcellular localization and enzyme family class, among many others...
  20. pmc PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
    Stephane Guindon
    Bioinformatics Institute and Allan Wilson Centre, University of Auckland Private Bag 92019, Auckland, New Zealand
    Nucleic Acids Res 33:W557-9. 2005
    ..The server and its documentation are available at http://atgc.lirmm.fr/phyml...
  21. ncbi SLLE for predicting membrane protein types
    Meng Wang
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 200030, China
    J Theor Biol 232:7-15. 2005
    ..The current approach represents a new strategy to deal with the problems of protein attribute prediction, and hence may become a useful vehicle in the area of bioinformatics and proteomics...
  22. pmc Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    Yanzhi Guo
    College of Chemistry, Sichuan University, Chengdu 610064 and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P R China
    Nucleic Acids Res 36:3025-30. 2008
    ..The prediction software and all data sets used in this article are freely available at http://www.scucic.cn/Predict_PPI/index.htm...
  23. pmc GeneSilico protein structure prediction meta-server
    Michal A Kurowski
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Nucleic Acids Res 31:3305-7. 2003
    ..The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta...
  24. pmc PROMALS3D: a tool for multiple protein sequence and structure alignments
    Jimin Pei
    Howard Hughes Medical Institute, Dallas, TX 75390, USA
    Nucleic Acids Res 36:2295-300. 2008
    ..PROMALS3D outperforms a number of existing methods for constructing multiple sequence or structural alignments using both reference-dependent and reference-independent evaluation methods...
  25. ncbi Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    Tal Pupko
    The Institute of Statistical Mathematics, 4 6 7 Minami Azabu, Minato ku, Tokyo 106 8569, Japan
    Bioinformatics 18:S71-7. 2002
    ..Functionally important regions often correspond to surface patches of slowly evolving residues...
  26. pmc BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
    Liangjiang Wang
    Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
    Nucleic Acids Res 34:W243-8. 2006
    ..BindN provides a useful tool for understanding the function of DNA and RNA-binding proteins based on primary sequence data...
  27. 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...
  28. pmc The PredictProtein server
    Burkhard Rost
    CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
    Nucleic Acids Res 32:W321-6. 2004
    ..For all services, users can submit their query either by electronic mail or interactively via the World Wide Web...
  29. ncbi Paircoil2: improved prediction of coiled coils from sequence
    A V McDonnell
    Mathematics Department, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA
    Bioinformatics 22:356-8. 2006
    ..Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure...
  30. pmc MEME: discovering and analyzing DNA and protein sequence motifs
    Timothy L Bailey
    Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    Nucleic Acids Res 34:W369-73. 2006
    ..This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance...
  31. pmc The MPI Bioinformatics Toolkit for protein sequence analysis
    Andreas Biegert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W335-9. 2006
    ..The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de...
  32. ncbi Proteomic analysis of post-translational modifications
    Matthias Mann
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK 5230 Denmark
    Nat Biotechnol 21:255-61. 2003
    ..Finally, stable isotope labeling strategies in combination with mass spectrometry have been applied successfully to study the dynamics of modifications...
  33. pmc Support vector machines for predicting membrane protein types by using functional domain composition
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    Biophys J 84:3257-63. 2003
    ..C. Chou (2001), may become a very useful high-throughput tool in the area of bioinformatics and proteomics...
  34. 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...
  35. ncbi Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence
    Georg Neuberger
    Research Institute of Molecular Pathology, Dr Bohrgasse 7, A 1030 Vienna, Austria
    J Mol Biol 328:581-92. 2003
    ..The predicted presence of a PTS1 signal implies peroxisomal localisation in the absence of N-terminal targeting sequences such as the mitochondrial import signal...
  36. 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...
  37. ncbi Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Bioinformatics 21:10-9. 2005
    ..Although the results were quite encouraging, the entire prediction process was based on the amino acid composition alone without including any sequence-order information. Therefore, it is worthy of further investigation...
  38. 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...
  39. pmc PrediSi: prediction of signal peptides and their cleavage positions
    Karsten Hiller
    Institut fur Mikrobiologie, Technische Universitat Braunschweig, Spielmannstrasse 7, D 38106 Braunschweig, Germany
    Nucleic Acids Res 32:W375-9. 2004
    ..PrediSi is accessible via a web interface. An extra Java package was designed for the integration of PrediSi into other software projects. The tool is freely available on the World Wide Web at http://www.predisi.de...
  40. 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...
  41. 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
    ....
  42. 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...
  43. 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
    ..The values of emPAI are easily calculated and add important quantitation information to proteomic experiments; therefore we suggest that they should be reported in large scale proteomic identification projects...
  44. 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...
  45. pmc SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
    C Z Cai
    Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
    Nucleic Acids Res 31:3692-7. 2003
    ..SVMProt can be accessed at http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi...
  46. pmc Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
    Christian Rausch
    Center for Bioinformatics Tübingen ZBIT, University of Tubingen, Germany
    Nucleic Acids Res 33:5799-808. 2005
    ..None of the predictive methods could infer any specificity for 2.4% of the sequences, suggesting completely new types of specificity...
  47. ncbi Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 23:3147-54. 2007
    ..Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications...
  48. pmc Kalign--an accurate and fast multiple sequence alignment algorithm
    Timo Lassmann
    Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S 17177 Stockholm, Sweden
    BMC Bioinformatics 6:298. 2005
    ..Current MSA methods suffer from being either too inaccurate or too computationally expensive to be applied effectively in large-scale comparative genomics...
  49. pmc NCBI Reference Sequence (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 33:D501-4. 2005
    ....
  50. ncbi A proteomics approach to understanding protein ubiquitination
    Junmin Peng
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Biotechnol 21:921-6. 2003
    ..The methodology described here provides a general tool for the large-scale analysis and characterization of protein ubiquitination...
  51. pmc DiANNA: a web server for disulfide connectivity prediction
    F Ferre
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    Nucleic Acids Res 33:W230-2. 2005
    ..Our novel neural network-based approach achieves results that are comparable and in some cases better than the current state-of-the-art methods...
  52. 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
    ....
  53. ncbi Predicting subcellular localization of proteins in a hybridization space
    Yu Dong Cai
    Biomolecular Sciences Department, UMIST, PO Box 88, Manchester M60 1QD, UK
    Bioinformatics 20:1151-6. 2004
    ....
  54. ncbi Heads or tails: a simple reliability check for multiple sequence alignments
    Giddy Landan
    Department of Biology and Biochemistry, University of Houston, TX, USA
    Mol Biol Evol 24:1380-3. 2007
    ..Surprisingly, Neighbor-Joining methods of phylogenetic reconstruction turned out to be less affected by alignment errors than maximum likelihood and Bayesian methods...
  55. ncbi Protein threading using PROSPECT: design and evaluation
    Y Xu
    Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830 6480, USA
    Proteins 40:343-54. 2000
    ..The system rigorously finds a globally optimal threading under the specified constraints. Test results have shown that the constraints can further improve the performance of PROSPECT. Proteins 2000;40:343-354...
  56. ncbi Subcellular location prediction of apoptosis proteins
    Guo Ping Zhou
    Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
    Proteins 50:44-8. 2003
    ....
  57. pmc Matt: local flexibility aids protein multiple structure alignment
    Matthew Menke
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 4:e10. 2008
    ..We postulate that Matt's strong performance comes from its ability to model proteins in different conformational states and, perhaps even more important, its ability to model backbone distortions in more distantly related proteins...
  58. pmc Phospho.ELM: a database of phosphorylation sites--update 2008
    Francesca Diella
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D240-4. 2008
    ..Phospho.ELM is available on line at: http://phospho.elm.eu.org...
  59. pmc A guided tour of the Trans-Proteomic Pipeline
    Eric W Deutsch
    Institute for Systems Biology, Seattle, WA, USA
    Proteomics 10:1150-9. 2010
    ....
  60. ncbi Porter: a new, accurate server for protein secondary structure prediction
    Gianluca Pollastri
    Computer Science Department, University College Dublin, Belfield, Dublin 4, Ireland
    Bioinformatics 21:1719-20. 2005
    ..Porter's accuracy, tested by rigorous 5-fold cross-validation on a large set of proteins, exceeds 79%, significantly above a copy of the state-of-the-art SSpro server, better than any system published to date...
  61. ncbi An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
    Mauro Delorenzi
    Genetics and Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
    Bioinformatics 18:617-25. 2002
    ..The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile...
  62. doi Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
    Oliver Schilling
    The UBC Centre for Blood Research, Department of Oral Biological and Medical Sciences, 4 401 Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    Nat Biotechnol 26:685-94. 2008
    ..Profiling of HIV protease 1, caspase 3, caspase 7, cathepsins K and G, elastase and thrombin showed that this approach is broadly applicable to all mechanistic classes of endoproteases...
  63. ncbi Selecton: a server for detecting evolutionary forces at a single amino-acid site
    Adi Doron-Faigenboim
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
    Bioinformatics 21:2101-3. 2005
    ..We test for the statistical significance of the site-specific scores in order to obtain reliable and valid estimates...
  64. ncbi Prediction of subcellular localization using sequence-biased recurrent networks
    Mikael Boden
    School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, Australia
    Bioinformatics 21:2279-86. 2005
    ..However, due to the low similarity of such sequences and the dynamical nature of the sorting process, the computational prediction of subcellular localization of proteins is challenging...
  65. pmc Comparative analysis of protein structure alignments
    Gabriele Mayr
    Department of Molecular Biology, University of Salzburg, Salzburg, Austria
    BMC Struct Biol 7:50. 2007
    ....
  66. pmc OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms
    Günther Zehetner
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Nucleic Acids Res 31:3799-803. 2003
    ..OntoBlast's web interface is accessible on the 'Ontologies TO GenomeMatrix Gate' page at http://functionalgenomics.de/ontogate/...
  67. ncbi FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded
    Jaime Prilusky
    Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 21:3435-8. 2005
    ..Sliding windows permit identification of large regions within a protein that possess folding propensities different from those of the whole protein...
  68. ncbi Convergent evolution of domain architectures (is rare)
    Julian Gough
    RIKEN Genomic Sciences Centre, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Bioinformatics 21:1464-71. 2005
    ..We use a range of methods including phylogenetic grouping, sequence similarity/alignment, mutation rates and comparative genomics to approach this difficult problem from several angles...
  69. ncbi The ABC's (and XYZ's) of peptide sequencing
    Hanno Steen
    Department of Systems Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nat Rev Mol Cell Biol 5:699-711. 2004
    ..The key - but little understood - technology in mass-spectrometry-based proteomics is peptide sequencing, which we describe and review here in an easily accessible format...
  70. 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...
  71. pmc Characterization and prediction of residues determining protein functional specificity
    John A Capra
    Department of Computer Science, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
    Bioinformatics 24:1473-80. 2008
    ..A number of sequence-based computational methods have been introduced for identifying SDPs; however, their further development and evaluation have been hindered by the limited number of known experimentally determined SDPs...
  72. pmc Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    Huiling Chen
    Department of Physics, Drexel University Philadelphia, PA 19104, USA
    Nucleic Acids Res 33:3193-9. 2005
    ..Of the total of 130 residues predicted as sites of deleterious mutations, 104 (or 80%) were correct...
  73. ncbi Prediction of protein B-factor profiles
    Zheng Yuan
    Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St Lucia, Australia
    Proteins 58:905-12. 2005
    ..flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods...
  74. pmc Length-dependent prediction of protein intrinsic disorder
    Kang Peng
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Bioinformatics 7:208. 2006
    ..However, these predictors are less successful on short disordered regions (< or =30 residues). A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions...
  75. pmc The PANTHER database of protein families, subfamilies, functions and pathways
    Huaiyu Mi
    Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA
    Nucleic Acids Res 33:D284-8. 2005
    ..Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com...
  76. ncbi Local structural disorder imparts plasticity on linear motifs
    Monika Fuxreiter
    Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary
    Bioinformatics 23:950-6. 2007
    ..These results establish a connection between LMs and molecular recognition elements of intrinsically unstructured proteins (IUPs), which realize a non-conventional mode of partner binding mostly in regulatory functions...
  77. ncbi 3D-Jury: a simple approach to improve protein structure predictions
    Krzysztof Ginalski
    BioInfoBank Institute, Limanowskiego 24A, 60 744 Poznan, Poland
    Bioinformatics 19:1015-8. 2003
    ..PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)..
  78. pmc The SLiMDisc server: short, linear motif discovery in proteins
    Norman E Davey
    UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
    Nucleic Acids Res 35:W455-9. 2007
    ..Returned motifs can also be compared with known SLiMs from the literature. SLiMDisc is available at: http://bioware.ucd.ie/~slimdisc/...
  79. ncbi RASCAL: rapid scanning and correction of multiple sequence alignments
    J D Thompson
    Laboratoire de Biologie et Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire CNRS INSERM ULP, B P 10142, 67404 Illkirch Cedex, France
    Bioinformatics 19:1155-61. 2003
    ..Alignment correction is then restricted to the less reliable regions, leading to a more reliable and efficient refinement strategy...
  80. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org...
  81. ncbi Probalign: multiple sequence alignment using partition function posterior probabilities
    Usman Roshan
    Department of Computer Science, New Jersey Institute of Technology GITC 4400, University Heights, NJ 07102, USA
    Bioinformatics 22:2715-21. 2006
    ..The partition function methodology is one way of estimating these probabilities. Here, we combine these two ideas for the first time to construct maximal expected accuracy sequence alignments...
  82. doi Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
    Benedict Paten
    Department of Engineering, University of California, Santa Cruz CA, USA
    Bioinformatics 25:295-301. 2009
    ..However, less work has been done in making promising methods that work on the small-scale practically for the alignment of much larger genomic sequences...
  83. 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
    ..In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular...
  84. ncbi CLANS: a Java application for visualizing protein families based on pairwise similarity
    Tancred Frickey
    Max Planck Institut fuer Entwicklungsbiologie, Spemannstrasse 35, 72076 Tuebingen, Germany
    Bioinformatics 20:3702-4. 2004
    ..AVAILABILITY: CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download...
  85. pmc 3D complex: a structural classification of protein complexes
    Emmanuel D Levy
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    PLoS Comput Biol 2:e155. 2006
    ..Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes...
  86. ncbi Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
    Lei Bao
    Department of Molecular Sciences, Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163, USA
    Bioinformatics 21:2185-90. 2005
    ..To facilitate the identification of disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the phenotypic effects of nsSNPs...
  87. pmc Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
    Nicolas Lartillot
    Laboratoire d Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS Université de Montpellier 2, Montpellier Cedex 5, France
    BMC Evol Biol 7:S4. 2007
    ....
  88. pmc DISULFIND: a disulfide bonding state and cysteine connectivity prediction server
    Alessio Ceroni
    Machine Learning and Neural Networks Group, Universita degli Studi di Firenze, Dipartimento di Sistemi e Informatica, Via di Santa Marta 3, 50139 Firenze, Italy
    Nucleic Acids Res 34:W177-81. 2006
    ..The output is a simple visualization of the assigned bonding state (with confidence degrees) and the most likely connectivity patterns. The server is available at http://disulfind.dsi.unifi.it/...
  89. pmc The Jpred 3 secondary structure prediction server
    Christian Cole
    School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
    Nucleic Acids Res 36:W197-201. 2008
    ..A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions...
  90. 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...
  91. ncbi Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
    Baoqiang Cao
    Biomedical Informatics, Children s Hospital Research Foundation, Cincinnati, OH 45229, USA
    Bioinformatics 22:303-9. 2006
    ..This offers the possibility of a more reliable estimation of the free parameters in the model with a limited number of experimentally resolved membrane protein structures...
  92. pmc GlobPlot: Exploring protein sequences for globularity and disorder
    Rune Linding
    European Molecular Biology Laboratory, Biocomputing Unit, D 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3701-8. 2003
    ..GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity...
  93. pmc LOMETS: a local meta-threading-server for protein structure prediction
    Sitao Wu
    Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 6604, USA
    Nucleic Acids Res 35:3375-82. 2007
    ..The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS...
  94. ncbi Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types
    Hongbin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Biochem Biophys Res Commun 334:288-92. 2005
    ..The OET-KNN classifier will be available as a web-server at http://www.pami.sjtu.edu.cn/kcchou...
  95. pmc I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
    Emidio Capriotti
    Laboratory of Biocomputing, CIRB Department of Biology, University of Bologna via Irnerio 42, 40126 Bologna, Italy
    Nucleic Acids Res 33:W306-10. 2005
    ..0 as a unique and valuable helper for protein design, even when the protein structure is not yet known with atomic resolution. Availability: http://gpcr.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi...
  96. ncbi Multiple flexible structure alignment using partial order graphs
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Bioinformatics 21:2362-9. 2005
    ..Understanding the structural divergence and flexibility is critical for studying the evolution of functions and specificities of proteins...
  97. pmc A network representation of protein structures: implications for protein stability
    K V Brinda
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
    Biophys J 89:4159-70. 2005
    ..Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability...
  98. pmc INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
    Sriram Sankararaman
    Department of Computer Science, University of California, Berkeley, USA
    Nucleic Acids Res 37:W390-5. 2009
    ..The INTREPID web server is available at http://phylogenomics.berkeley.edu/intrepid...
  99. pmc Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling
    Timothy E Gookin
    Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Genome Biol 9:R120. 2008
    ....
  100. ncbi AMPer: a database and an automated discovery tool for antimicrobial peptides
    Christopher D Fjell
    Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
    Bioinformatics 23:1148-55. 2007
    ..with up to 99% accuracy and can be used for discovering novel AMP candidates...
  101. pmc PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
    Joshua L Heazlewood
    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia
    Nucleic Acids Res 36:D1015-21. 2008
    ..The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt) provides a valuable resource to the plant science community and can be accessed through the following link http://phosphat.mpimp-golm.mpg.de...

Research Grants63

  1. NON-GASTRIN ACID SECRETAGOGUE IN ISLET CELL TUMORS
    William Chey; Fiscal Year: 1990
    ..Immunoreactive NGAS contents will be determined in islet cell tumors also. Finally, release of NGAS in response to a meat meal will be studied in dogs...
  2. ALDEHYDE DEHYDROGENASE AND PATHOGENESIS OF ALCOHOLISM
    REGINA PIETRUSZKO; Fiscal Year: 1993
    ..Development of monoclonal antibodies and radioimmunoassay capable to determining precisely the individual E1, E2 and E3 isozymes in the crude tissue homogenates is also envisaged...
  3. DIABETES MELLITUS & ISLET AMYLOID POLYPEPTIDE (IAAP)
    Kenneth Johnson; Fiscal Year: 1991
    ..Amyloid samples will be purified by size exclusion and revered phase HPLC for subsequent amino acid sequencing...
  4. Signal Transduction Mechanisms in Ocular Albinism
    Vinit Mahajan; Fiscal Year: 2005
    ..Under the mentorship of Dr. Debora Farber, I hope to launch an academic career and establish a research laboratory aimed at understanding and treating retinal disease. ..
  5. ROLE OF AEROMONAS HYDROPHILA VIRULENCE FACTORS
    CLIFFORD HOUSTON; Fiscal Year: 1992
    ..The proposed research involving CTC cytolysin and non-CTC enterotoxin as well as other virulence factors may aid in elucidating the means by which A. hydrophila cause human disease...
  6. DOXORUBICIN BIOSYNTHESIS AND RESISTANCE
    CHARLES SIH; Fiscal Year: 2000
    ..If not, then the applicants will determine if the expression of selected dnr structural genes is controlled by phosphate level, with or without dnrN or dnrI involvement. ..
  7. ROLE OF THYROGLOBULIN IN THYROXINE BIOSYNTHESIS
    ALLEN RAWITCH; Fiscal Year: 1990
    ..The structure and function of thyroid peroxidase are being studied along with new methodology for its purification...
  8. CA2+ RELEASE CHANNEL FROM CARDIAC SARCOPLASMIC RETICULUM
    Kevin Campbell; Fiscal Year: 1991
    ....
  9. REGULATION OF TRACHEA MUCIN SYNTHESIS AND GLYCOSYLATION
    Joseph Mendicino; Fiscal Year: 1990
    ..These preliminary studies provide considerable encouragement for success of the studies described in this application...
  10. CLONING OF THE HUMAN RECEPTOR FOR ALPHA-2-INTERFERON
    LINVILLE MEADOWS; Fiscal Year: 1990
    ..The research facilities within the School of Medicine and the Lineberger Cancer Center will provide an excellent environment for Dr. Meadows to complete his basic research training in molecular biology...
  11. PERITONEAL MACROPHAGE MIGRATION IN ENDOMETRIOSIS
    CECIL LYTTLE; Fiscal Year: 1993
    ....
  12. HUMORAL FACTORS IN INFLAMMATION
    TONY HUGLI; Fiscal Year: 1993
    ..Probes designed from protein sequence analysis will be used for complete molecular analysis of the membrane component...
  13. C-Reactive Protein in Human Mucosal Immunity
    Jane Gould; Fiscal Year: 2005
    ..These results will be tested in vivo using murine models of respiratory tract infection with mice carrying the human CRP transgene. ..
  14. SEQUENCING OF CLASS I MHC PEPTIDES BY MASS SPECTROMETRY
    Robert Cotter; Fiscal Year: 1999
    ..Finally, we describe two new projects that are now underway: the identification of MHC class I peptides associated with MMTV-infected mouse mammary tumor cells, and natural ligands recognized during T-cell selection in the thymus. ..
  15. RECEPTOR MUTANTS IN VITAMIN D RESISTANT RICKETS OF BONE
    Mark Hughes; Fiscal Year: 1991
    ..Similarly, mutations involving hormone binding affinity will be studied to define in molecular terms the steroid binding pocket and the critical amino acids involved in ligand interaction on with the receptor...
  16. BIOCHEMICAL STUDIES ON THE LH-HCG RECEPTOR
    Brij Saxena; Fiscal Year: 1990
    ..These studies are vital to understand the mechanism of hormone action at the molecular level during normal and abnormal gonadal function...
  17. MOLECULAR STUDIES OF A KEY BILE ACID METABOLIZING ENZYME
    Andrew Stolz; Fiscal Year: 1993
    ..These studies will significantly advance the characterization of the 3 alpha HSD and its physiological regulation. The work proposed will lay the foundation for more advanced studies on the regulation of this protein in future studies...
  18. STRUCTURE/FUNCTION OF RAGWEED POLLEN ALLERGEN ANTIGEN E
    David Klapper; Fiscal Year: 1992
    ..Western" and "dot" blotting procedures ensure that a particular message is present prior to synthesizing a cDNA library for sequence analysis and placement into expression vectors...
  19. BLOOD PLASMA PROTEINS--STRUCTURE AND FUNCTION
    Frank Putnam; Fiscal Year: 1993
    ..b>Protein sequence analysis is being used to determine the structural chances in human serum albumin in more than 100 serum ..
  20. ANALYSIS OF NON-SMALL CELL LUNG CARCINOMA ANTIGENS
    PER PETERSON; Fiscal Year: 1990
    ....
  21. Functional Analysis of A Novel Prostate-Associated Gene
    Yi Lu; Fiscal Year: 2005
    ..showed that (1) pHyde causes growth inhibition and induces apoptosis in prostate cancer cells; (2) The protein sequence analysis indicates that hpHyde may be a transmembrane protein and it shares a similar secondary structure with ..
  22. REGULATION OF MYOCARDIAL SYNTHESIS, RELEASE & PROCESSING
    James Greenwald; Fiscal Year: 1993
    ..Hopefully, these experiments will clarify approaches to pharmacologically manipulate atriopeptin synthesis, storage and release in pathophysiological states...
  23. KERATOCYTE CRYSTALLIN PROTEINS AND CORNEAL TRANSPARENCY
    JAMES JESTER; Fiscal Year: 2003
    ....
  24. STUDIES ON SIGMA RECEPTORS AND THEIR LIGANDS
    Eckard Weber; Fiscal Year: 1993
    ....
  25. PEPTIDE/PROTEIN ANALYSIS FACILITY
    C Kahn; Fiscal Year: 1991
    ..In recent years, the scope of protein sequence analysis has changed from the aim of determining the complete primary structure of a protein by sequence analysis ..
  26. NOVEL PROTEIN KINASE IN DIGESTIVE ENZYME SECRETION
    Laura Tang; Fiscal Year: 1999
    ..The elucidation of the mechanism of zymogen secretion will facilitate the identification of its relevance to human disease processes. The ability to regulate zymogen secretion may become an important therapeutic strategy. ..
  27. INTERACTIONS OF C1Q WITH PHAGOCYTIC CELLS
    WILSON BURGESS; Fiscal Year: 1991
    ..Ultimately, this research should aid in the development of beneficial therapeutic or prophylactic procedures to augment appropriate protective responses...
  28. FUNCTION OF 13-CIS-RETINOIC ACID IN HL-60 CELLS
    Malford Cullum; Fiscal Year: 1992
    ..Gene expression will be assessed at the cellular level by correlating the subcellular localization of 13cisretinoic acid and the ability to differentiate in HL60 and in constructed HL60 variants...
  29. 2NOVEL EMBRYONIC GENES AND LIVER DEVELOPMENT
    Lopa Mishra; Fiscal Year: 1999
    ....
  30. NOVEL GLYCOCONJUGATE-BINDING PROTEINS OF LEUCOCYTES
    HOWARD ALLEN; Fiscal Year: 1990
    ..These studies will lay the necessary foundation to pursue the elucidation of carbohydrate-binding protein function and how pertubation of function affects cell behavior...
  31. Investigation of influenza virulence mediated by the NS1A protein
    DIANA NOAH; Fiscal Year: 2007
    ..in the NS1A protein leads to a substantially increased rate of virus-specific RNA synthesis, 3) recent protein sequence analysis places the nuclear export signal of NS1A in the virulence region identified above, and 4) the NS1A L77A ..
  32. Role of LIBC in Inflammatory Breast Cancer Phenotype
    Celina Kleer; Fiscal Year: 2007
    ..Also, understanding the role of WISP3 will shed light on the mechanisms of cancer development in general and serve as a model for other related CCN genes involved in carcinogenesis. ..
  33. LIPID ALDEHYDES AND ETHANOL INDUCED LIVER DAMAGE
    DENNIS PETERSEN; Fiscal Year: 2005
    ..Identification of susceptible cellular targets and specific mechanisms could provide information leading to the development of effective therapeutic interventions for altering specific events involved in ALD. ..
  34. STRUCTURE AND BIOLOGICAL FUNCTION OF THE MONOKINE ECEF
    David Silberstein; Fiscal Year: 1993
    ..The effects of ECEF on other types of inflammatory cells will be evaluated, using functional and receptor binding assays...
  35. Molecular Dissection of Hepatitis C Virus Replicase
    Guangxiang Luo; Fiscal Year: 2006
    ..abstract_text> ..
  36. PX REGION OF HTLV I AND II
    William Haseltine; Fiscal Year: 1992
    ..aims include: a) development of specific antisera to the separate coding regions of pp27 and pp21; b) protein sequence analysis of the pp27 and pp21 proteins; c) characterization of the pp27 and pp21 messenger RNA species; d) large ..
  37. TRANSCRIPTIONAL REGULATION DURING SPERMATOGENESIS
    SIDNEY GRIMES; Fiscal Year: 1999
    ..To determine the role of the TE-binding protein in regulating testis-specific transcription, its activity will be examined in transcription assays. ..
  38. Discovery of soluble HIV suppressor factors
    Fiorenza Cocchi; Fiscal Year: 2006
    ..Mixtures of cognate antibodies will be used in cases where we have evidence that several antiviral factors mediate redundant antiviral activity. ..
  39. STRUCTURE AND GENETICS OF ANTIBODY VARIABLE REGIONS
    LOVICK CANNON; Fiscal Year: 1980
    ....
  40. Sixth International Uppsala Conference on Electron Capture and Transfer Dissociat
    Joshua Coon; Fiscal Year: 2009
    ..ECD and its offspring, electron transfer dissociation (ETD), have become key players in the field of protein sequence analysis. The methods are proving critical for biological applications ranging from intact protein sequencing (..
  41. BioHDF - Open Binary File Standards for Bioinformatics
    Todd Smith; Fiscal Year: 2005
    ..The envisioned framework will integrate algorithms important in DNA and protein sequence analysis to create scalable high throughput software systems which will be accessed using new graphical user ..
  42. Linear Ion Trap for Proteomics
    Paul Stemmer; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  43. 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...
  44. FUNCTION OF AN APP CYTOPLASMIC DOMAIN BINDING PROTEIN
    I Shapiro; Fiscal Year: 1999
    ..These studies will investigate a novel finding and a new aspect of the regulation of APP processing and should have a direct impact on understanding APP processing and possibly AD pathogenesis. ..
  45. FIBRINOGEN VARIANTS--STRUCTURE AND FUNCTION
    Agnes Henschen Edman; Fiscal Year: 1993
    ..The correlation between the structural-functional properties of the isolated abnormal fibrinogen variants and clinical observations in the respective families will be analyzed...
  46. COMPUTATIONAL APPROACHES TO PROTEIN SEQUENCE ANALYSIS
    David States; Fiscal Year: 2004
    ..These models will be used to explore which protein properties are likely to be inherent, and to understand how much information can be derived for proteins based on information about known homologs. ..
  47. HTLV-I: STUDY OF HOST-VIRUS INTERACTIONS
    Thomas Palker; Fiscal Year: 1993
    ..RIA and immunoblot assays will be used to evaluate the prevalence of HTLV- I infection in AIDS patients, in hemophiliacs and in individuals from STD clinics in North Carolina...
  48. PROTEIN ANALYSIS BY THERMOSPRAY MASS SPECTROMETRY
    DOUGLAS DYCKES; Fiscal Year: 1990
    The purpose of this research is to refine a rapid method of protein sequence analysis which uses enzyme technology and thermospray mass spectrometry in a continuous flow system...
  49. ALDOSE REDUCTASE AND DIABETIC COMPLICATIONS
    SATISH SRIVASTAVA; Fiscal Year: 2002
    ..The PI results should show whether inclusions of antioxidants as part of ARI therapy in diabetes would be useful to counteract and decrease in cellular antioxidant defense due to inhibition of AR. ..
  50. ANTIGENURIA--EXPERIMENTAL & HUMAN MYCOBACTERIAL INFECT
    Robert Wallis; Fiscal Year: 2000
    ..This project may ultimately lead to the development of a novel assay which can be used clinically for diagnosis and management of latent and active mycobacterial infection in AIDS. ..
  51. INTESTINAL CELL DIFFERENTIATION IN VIVO AND IN CULTURE
    Andrea Quaroni; Fiscal Year: 1991
    ....
  52. BIOENERGETIC APPARATUS IN HEART MITOCHONDRIA
    TSOO KING; Fiscal Year: 1990
    ..It should be pointed out that this application (which differs from another project) emphasizes and deals with aspects of the non-cytochrome-containing components of the respiratory chain...
  53. SIGNAL TRANSDUCTION IN SALIVARY GLAND
    Norman Boyd; Fiscal Year: 1993
    ..There are disease states that result from altered G protein function. Understanding the role of G in the phosphoinositide/Ca2+ pathway will permit an assessment of altered transduction in certain states of salivary gland dysfunction...
  54. ANTIGEN PROCESSING GENES AND CELL BIOLOGY
    TOM COTNER; Fiscal Year: 2001
    ..constructs, gel shift assays, DM mRNA stability and, when the affected genes are identified, by DNA and protein sequence analysis for domains and motifs informative regarding function, by expression of the protein products of the ..
  55. CELL PATHOLOGY IN KIDNEY HYPOXIA. ROLE OF BAX
    Pothana Saikumar; Fiscal Year: 2007
    ..In vivo gene silencing of Bax will be attempted in efforts to block up regulation of Bax and thereby prevent cell injury in the ischemic kidney. ..
  56. BIOMEDICAL RESEARCH SUPPORT
    HERBERT DICKERMAN; Fiscal Year: 1991
    ..g., amino acid analysis and protein sequence analysis) and mass spectrometry...
  57. 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. ..
  58. The role of viral diversity in HIV-1 drug resistance
    Manish Sagar; Fiscal Year: 2006
    ..With these studies, we will gain insight into the likelihood of success with ART in Africa and the possibility of the evolution of a 'new' epidemic with drug resistant HIV -1 viruses. ..
  59. An integrated approach to infer and validate domain-domain interactions in protei
    Chittibabu Guda; Fiscal Year: 2008
    ..The methodology and data generated in this project can help understand the functional basis of protein-protein interactions, with a multitude of implications in systems biology research. [unreadable] [unreadable] [unreadable]..
  60. Algorithms for protein superfamily classification and function prediction
    Degui Zhi; Fiscal Year: 2008
    ..Our computational approach will speed up the discovery of biological knowledge from large data sets generated by high-throughput methods. [unreadable] [unreadable] [unreadable]..
  61. Modeling of Protein Complexes and Missense Mutations
    Roland Dunbrack; Fiscal Year: 2009
    ..These interactions may be compromised by missense mutations that alter individual interactions between molecules or mutations that lower protein stability. ..
  62. Identifying Ubiquitin E3 Substrates with Redesigned E3s
    Brian Kuhlman; Fiscal Year: 2005
    ..Favorable results will indicate that this new method should be an excellent approach for identifying substrates of other E3 ubiquitin ligases important to health and disease. ..
  63. Sequence alignment fidelity in genomics and bioinformatics
    Michael S Rosenberg; Fiscal Year: 2010
    ....