Genomes and Genes
Affiliation: Lawrence Livermore National Laboratory
- STRALCP--structure alignment-based clustering of proteinsAdam 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...
- A study of quality measures for protein threading modelsS 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...
- LGA: A method for finding 3D similarities in protein structuresAdam 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...
- Comparative genomics tools applied to bioterrorism defenceTom Slezak
Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Brief Bioinform 4:133-49. 2003....
- Identification of a thermo-regulated glutamine-binding protein from Yersinia pestisMonique 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...
- SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studiesAnu 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...
- The TB structural genomics consortium crystallization facility: towards automation from protein to electron densityBernhard 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...
- Selective high-affinity ligand antibody mimics for cancer diagnosis and therapy: initial application to lymphoma/leukemiaRod Balhorn
Chemistry, Materials and Life Sciences and Computations, Lawrence Livermore National Laboratory, Livermore, California, 94550, USA
Clin Cancer Res 13:5621s-5628s. 2007....
- Assessment of progress over the CASP experimentsCeslovas 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...
- The role of viral population diversity in adaptation of bovine coronavirus to new host environmentsMonica K Borucki
Lawrence Livermore National Laboratory, Livermore, California, United States of America
PLoS ONE 8:e52752. 2013....
- Practical applications of structural genomics technologies for mutagen researchAdam 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...
- Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial communitySteven W Singer
Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Appl Environ Microbiol 74:4454-62. 2008....
- Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathwayKatherine 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...
- The significance of performance ranking in CASP--response to Marti-Renom et alJohn Moult
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA
Structure 10:291-2; discussion 292-3. 2002
- The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigensBrian 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...
- Antibody elbow angles are influenced by their light chain classRobyn 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...
- Critical assessment of methods of protein structure prediction (CASP)-round VJohn 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...