Adam Zemla

Summary

Affiliation: Lawrence Livermore National Laboratory
Country: USA

Publications

  1. pmc STRALCP--structure alignment-based clustering of proteins
    Adam Zemla
    Computing Applications and Research, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Nucleic Acids Res 35:e150. 2007
  2. pmc AS2TS system for protein structure modeling and analysis
    A Zemla
    Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
    Nucleic Acids Res 33:W111-5. 2005
  3. pmc A study of quality measures for protein threading models
    S Cristobal
    Cell and Molecular Biology Department, Box 596 BMC Uppsala University, SE 751 24 Uppsala, Sweden
    BMC Bioinformatics 2:5. 2001
  4. 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
  5. ncbi request reprint Comparative genomics tools applied to bioterrorism defence
    Tom Slezak
    Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Brief Bioinform 4:133-49. 2003
  6. ncbi request reprint Identification of a thermo-regulated glutamine-binding protein from Yersinia pestis
    Monique Cosman
    Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Protein Pept Lett 15:887-94. 2008
  7. ncbi request reprint Assessment of progress over the CASP experiments
    Ceslovas Venclovas
    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California, USA
    Proteins 53:585-95. 2003
  8. pmc The role of viral population diversity in adaptation of bovine coronavirus to new host environments
    Monica K Borucki
    Lawrence Livermore National Laboratory, Livermore, CA, USA
    PLoS ONE 8:e52752. 2013
  9. pmc SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies
    Anu Chakicherla
    Computing Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, California, United States of America
    PLoS Comput Biol 5:e1000401. 2009
  10. ncbi request reprint Selective high-affinity ligand antibody mimics for cancer diagnosis and therapy: initial application to lymphoma/leukemia
    Rod Balhorn
    Chemistry, Materials and Life Sciences and Computations, Lawrence Livermore National Laboratory, Livermore, California, 94550, USA
    Clin Cancer Res 13:5621s-5628s. 2007

Detail Information

Publications18

  1. pmc STRALCP--structure alignment-based clustering of proteins
    Adam Zemla
    Computing Applications and Research, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Nucleic Acids Res 35:e150. 2007
    ..We also provide a web server at http://as2ts.llnl.gov/AS2TS/STRALCP/ for selecting protein structures, calculating structurally conserved regions and performing automated clustering...
  2. pmc AS2TS system for protein structure modeling and analysis
    A Zemla
    Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
    Nucleic Acids Res 33:W111-5. 2005
    ..g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at http://as2ts.llnl.gov/...
  3. pmc A study of quality measures for protein threading models
    S Cristobal
    Cell and Molecular Biology Department, Box 596 BMC Uppsala University, SE 751 24 Uppsala, Sweden
    BMC Bioinformatics 2:5. 2001
    ..These measures include the measures used in CASP3 and CASP2 as well as have measures introduced later. We have studied their ability to distinguish between the better and worse models submitted to CASP3 and the correlation between them...
  4. 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...
  5. ncbi request reprint Comparative genomics tools applied to bioterrorism defence
    Tom Slezak
    Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Brief Bioinform 4:133-49. 2003
    ....
  6. ncbi request reprint Identification of a thermo-regulated glutamine-binding protein from Yersinia pestis
    Monique Cosman
    Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Protein Pept Lett 15:887-94. 2008
    ..The identification and characterization of an unknown protein function using the strategy presented here has applicability to a variety of research areas, including functional genomics and proteomics efforts...
  7. ncbi request reprint Assessment of progress over the CASP experiments
    Ceslovas Venclovas
    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California, USA
    Proteins 53:585-95. 2003
    ..Although specific progress between successive experiments is sometimes difficulty to identify, over the history of all the CASPs there has been steady, if sometimes slow, progress in all modeling regimes...
  8. pmc The role of viral population diversity in adaptation of bovine coronavirus to new host environments
    Monica K Borucki
    Lawrence Livermore National Laboratory, Livermore, CA, USA
    PLoS ONE 8:e52752. 2013
    ....
  9. pmc SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies
    Anu Chakicherla
    Computing Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, California, United States of America
    PLoS Comput Biol 5:e1000401. 2009
    ..Our domain-fusion algorithm leverages quantitative structure information and provides a tool for generation of hypotheses regarding protein function, which can then be tested using empirical methods...
  10. ncbi request reprint Selective high-affinity ligand antibody mimics for cancer diagnosis and therapy: initial application to lymphoma/leukemia
    Rod Balhorn
    Chemistry, Materials and Life Sciences and Computations, Lawrence Livermore National Laboratory, Livermore, California, 94550, USA
    Clin Cancer Res 13:5621s-5628s. 2007
    ....
  11. ncbi request reprint The TB structural genomics consortium crystallization facility: towards automation from protein to electron density
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Acta Crystallogr D Biol Crystallogr 58:1514-8. 2002
    ..Modular design of robotics and automated scripts using publicly available programs for structure solution allow for efficient high throughput crystallography - at a reasonable cost...
  12. doi request reprint Practical applications of structural genomics technologies for mutagen research
    Adam Zemla
    Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94551 0808, USA
    Mutat Res 722:165-70. 2011
    ..Better functional annotation can inform pathway and systems biology models...
  13. pmc Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community
    Steven W Singer
    Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
    Appl Environ Microbiol 74:4454-62. 2008
    ....
  14. ncbi request reprint The significance of performance ranking in CASP--response to Marti-Renom et al
    John Moult
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA
    Structure 10:291-2; discussion 292-3. 2002
  15. ncbi request reprint The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens
    Brian V Geisbrecht
    Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Biol Chem 280:17243-50. 2005
    ..These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships...
  16. ncbi request reprint Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry and W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA
    Acta Crystallogr D Biol Crystallogr 60:895-902. 2004
    ..The 1.7 A native structure determined by the consortium facilities is reported and implications for in silico screening of ligands for structure-guided drug design are discussed...
  17. ncbi request reprint Critical assessment of methods of protein structure prediction (CASP)-round V
    John Moult
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
    Proteins 53:334-9. 2003
    ..A brief summary of progress over the five CASP experiments is provided. Related developments in the field are also described...
  18. ncbi request reprint Antibody elbow angles are influenced by their light chain class
    Robyn L Stanfield
    Department of Molecular Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 357:1566-74. 2006
    ..A new, web-based computer program that was used to calculate the Fab elbow angles is described...