Experts and Doctors on protein sequence analysis in Bethesda, Maryland, United States


Locale: Bethesda, Maryland, United States
Topic: protein sequence analysis

Top Publications

  1. Whalley T, Timmers K, Coorssen J, Bezrukov L, Kingsley D, Zimmerberg J. Membrane fusion of secretory vesicles of the sea urchin egg in the absence of NSF. J Cell Sci. 2004;117:2345-56 pubmed publisher
    ..In contrast, isolated CVs, though all capable of Ca(2+)-triggered homotypic fusion, contain less than one hexamer of NSF per CV. Thus NSF is not a required component of the CV fusion machinery...
  2. Morgulis A, Coulouris G, Raytselis Y, Madden T, Agarwala R, Schäffer A. Database indexing for production MegaBLAST searches. Bioinformatics. 2008;24:1757-64 pubmed publisher [corrected] Supplementary data are available at Bioinformatics online. ..
  3. Sam V, Tai C, Garnier J, Gibrat J, Lee B, Munson P. ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. BMC Bioinformatics. 2006;7:206 pubmed
    ..Others may be intrinsic to the problem, suggesting a continuous rather than discrete protein fold space. ..
  4. Sam V, Tai C, Garnier J, Gibrat J, Lee B, Munson P. Towards an automatic classification of protein structural domains based on structural similarity. BMC Bioinformatics. 2008;9:74 pubmed publisher
    ..None of the tested procedures completely eliminates the divergence between automatic and manual protein classifications. Achieving full agreement between these two approaches would apparently require additional information. ..
  5. Thangudu R, Tyagi M, Shoemaker B, Bryant S, Panchenko A, Madej T. Knowledge-based annotation of small molecule binding sites in proteins. BMC Bioinformatics. 2010;11:365 pubmed publisher
    ..The method can be applied even for a query sequence without structure. The method is available at ..
  6. Venancio T, Aravind L. CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes. Bioinformatics. 2010;26:149-52 pubmed publisher
    ..Thus, CYSTM proteins are likely to be part of a novel cellular protective mechanism that is widely active in eukaryotes, including humans. Supplementary data are available at Bioinformatics online. ..
  7. Wu X, Zhou T, O Dell S, Wyatt R, Kwong P, Mascola J. Mechanism of human immunodeficiency virus type 1 resistance to monoclonal antibody B12 that effectively targets the site of CD4 attachment. J Virol. 2009;83:10892-907 pubmed publisher
  8. Galperin M. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol. 2006;188:4169-82 pubmed
    ..The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at ..
  9. Kim C, Tai C, Lee B. Iterative refinement of structure-based sequence alignments by Seed Extension. BMC Bioinformatics. 2009;10:210 pubmed publisher

More Information


  1. Kehrl J, Srikumar D, Harrison K, Wilson G, Shi C. Additional 5' exons in the RGS3 locus generate multiple mRNA transcripts, one of which accounts for the origin of human PDZ-RGS3. Genomics. 2002;79:860-8 pubmed
    ..For each RGS3 isoform, RT-PCR detected specific mRNA transcripts and immunoblot analysis identified specific bands for RGS3 and PDZ-RGS3. RGS3 provides an example of the complex origins of the coding regions of mammalian proteins. ..
  2. McKnight D, Simmer J, Hart P, Hart T, Fisher L. Overlapping DSPP mutations cause dentin dysplasia and dentinogenesis imperfecta. J Dent Res. 2008;87:1108-11 pubmed
    ..Furthermore, the consistent kindred presentation of the DD or DGI phenotype appears to be dependent on an as-yet-undescribed genetic modifier closely linked to DSPP. ..
  3. Zhang P, Zhang J, Sheng H, Russo J, Osborne B, Buetow K. Gene functional similarity search tool (GFSST). BMC Bioinformatics. 2006;7:135 pubmed
    ..This represents a powerful new approach for selecting similar genes and gene products from proteome databases according to their functions. ..
  4. Tai C, Vincent J, Kim C, Lee B. SE: an algorithm for deriving sequence alignment from a pair of superimposed structures. BMC Bioinformatics. 2009;10 Suppl 1:S4 pubmed publisher
    ..The Seed Extension algorithm is fast and, without using a gap penalty, produces more accurate sequence alignments from superimposed structures than three other programs tested that use dynamic programming algorithm. ..
  5. Guimarães K, Przytycka T. Interrogating domain-domain interactions with parsimony based approaches. BMC Bioinformatics. 2008;9:171 pubmed publisher
  6. Liu Y, Wang Z, Thomas J, Goodwin K, Stavrou S, Neville D. Polymorphisms of CD3epsilon in cynomolgus and rhesus monkeys and their relevance to anti-CD3 antibodies and immunotoxins. Immunol Cell Biol. 2007;85:357-62 pubmed
  7. Chakrabarti S, Lanczycki C, Panchenko A, Przytycka T, Thiessen P, Bryant S. State of the art: refinement of multiple sequence alignments. BMC Bioinformatics. 2006;7:499 pubmed
    ..In most cases REFINER produces a higher-scoring, modestly improved alignment that does not deteriorate the well-conserved regions of the original alignment. ..
  8. Moon K, Hood B, Kim B, Hardwick J, Conrads T, Veenstra T, et al. Inactivation of oxidized and S-nitrosylated mitochondrial proteins in alcoholic fatty liver of rats. Hepatology. 2006;44:1218-30 pubmed
    ..In conclusion, our results help to explain the underlying mechanism for mitochondrial dysfunction and increased susceptibility to alcohol-mediated liver damage. ..
  9. Lowenthal M, Mehta A, Frogale K, Bandle R, Araujo R, Hood B, et al. Analysis of albumin-associated peptides and proteins from ovarian cancer patients. Clin Chem. 2005;51:1933-45 pubmed
    ..Carrier-protein harvesting provides a rich source of candidate peptides and proteins with potential diverse tissue and cellular origins that may reflect important disease-related information. ..
  10. Bera T, Hahn Y, Lee B, Pastan I. TEPP, a new gene specifically expressed in testis, prostate, and placenta and well conserved in chordates. Biochem Biophys Res Commun. 2003;312:1209-15 pubmed
    ..Selective expression of TEPP in testis, prostate, and in placenta and its high conservation among different species indicate that TEPP might have a role in reproductive biology. ..
  11. Chen S, Samuel W, Fariss R, Duncan T, Kutty R, Wiggert B. Differentiation of human retinal pigment epithelial cells into neuronal phenotype by N-(4-hydroxyphenyl)retinamide. J Neurochem. 2003;84:972-81 pubmed
    ..Thus, fenretinide, a synthetic retinoid, is able to induce neuronal differentiation of human RPE cells in culture. ..
  12. Marchler Bauer A, Anderson J, Chitsaz F, Derbyshire M, DeWeese Scott C, Fong J, et al. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009;37:D205-10 pubmed publisher