molecular structure

Summary

Summary: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.

Top Publications

  1. 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
  2. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
  3. ncbi Crystallography & NMR system: A new software suite for macromolecular structure determination
    A T Brunger
    The Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
    Acta Crystallogr D Biol Crystallogr 54:905-21. 1998
  4. ncbi PHENIX: building new software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 4 230, Berkeley, CA 94720, USA
    Acta Crystallogr D Biol Crystallogr 58:1948-54. 2002
  5. ncbi Natural products as sources of new drugs over the last 25 years
    David J Newman
    Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute Frederick, P O Box B, Frederick, MD 21702, USA
    J Nat Prod 70:461-77. 2007
  6. pmc Comprehensive molecular structure of the eukaryotic ribosome
    Derek J Taylor
    Wadsworth Center, Empire State Plaza, Albany, NY 12201 0509, USA
    Structure 17:1591-604. 2009
  7. pmc ZINC--a free database of commercially available compounds for virtual screening
    John J Irwin
    Department of Pharmaceutical Chemistry, University of California San Francisco, Genentech Hall, 600 16th Street, San Francisco, California 94143, USA
    J Chem Inf Model 45:177-82. 2005
  8. ncbi Cytotoxic and anti-inflammatory cembranoids from the soft coral Lobophytum crassum
    Chih Hua Chao
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 71:1819-24. 2008
  9. pmc PubChem: a public information system for analyzing bioactivities of small molecules
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:W623-33. 2009
  10. ncbi Unprecedented hemiketal cembranolides with anti-inflammatory activity from the soft coral Lobophytum durum
    Shi Yie Cheng
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 72:152-5. 2009

Research Grants

Detail Information

Publications401 found, 100 shown here

  1. 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...
  2. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    ..This service is available free to all users at http://molprobity.biochem.duke.edu...
  3. ncbi Crystallography & NMR system: A new software suite for macromolecular structure determination
    A T Brunger
    The Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
    Acta Crystallogr D Biol Crystallogr 54:905-21. 1998
    ..User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR...
  4. ncbi PHENIX: building new software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 4 230, Berkeley, CA 94720, USA
    Acta Crystallogr D Biol Crystallogr 58:1948-54. 2002
    ..This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer...
  5. ncbi Natural products as sources of new drugs over the last 25 years
    David J Newman
    Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute Frederick, P O Box B, Frederick, MD 21702, USA
    J Nat Prod 70:461-77. 2007
    ....
  6. pmc Comprehensive molecular structure of the eukaryotic ribosome
    Derek J Taylor
    Wadsworth Center, Empire State Plaza, Albany, NY 12201 0509, USA
    Structure 17:1591-604. 2009
    ..Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2...
  7. pmc ZINC--a free database of commercially available compounds for virtual screening
    John J Irwin
    Department of Pharmaceutical Chemistry, University of California San Francisco, Genentech Hall, 600 16th Street, San Francisco, California 94143, USA
    J Chem Inf Model 45:177-82. 2005
    ..Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists...
  8. ncbi Cytotoxic and anti-inflammatory cembranoids from the soft coral Lobophytum crassum
    Chih Hua Chao
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 71:1819-24. 2008
    ..Compounds 1, 3, 7, and 10 were found to inhibit the accumulation of the pro-inflammatory proteins iNOS and COX-2 at 10 μM...
  9. pmc PubChem: a public information system for analyzing bioactivities of small molecules
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:W623-33. 2009
    ..Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually...
  10. ncbi Unprecedented hemiketal cembranolides with anti-inflammatory activity from the soft coral Lobophytum durum
    Shi Yie Cheng
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 72:152-5. 2009
    ..Full NMR spectroscopic assignments are provided for all isolated metabolites. The anti-inflammatory activities of 1-3 were evaluated in vitro...
  11. ncbi The Xplor-NIH NMR molecular structure determination package
    Charles D Schwieters
    Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, 20892 5624, Bethesda, MD, USA
    J Magn Reson 160:65-73. 2003
    ..Support for these scripting languages also facilitates interaction with existing external programs for structure analysis, structure manipulation, visualization, and spectral analysis...
  12. pmc Small-molecule correctors of defective DeltaF508-CFTR cellular processing identified by high-throughput screening
    Nicoletta Pedemonte
    Department of Medicine, UCSF, San Francisco, California 94143 0521, USA
    J Clin Invest 115:2564-71. 2005
    ..Small-molecule correctors may be useful in the treatment of CF caused by the DeltaF508 mutation...
  13. pmc N-myristoyltransferase inhibitors as new leads to treat sleeping sickness
    Julie A Frearson
    Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
    Nature 464:728-32. 2010
    ..Our studies validate T. brucei N-myristoyltransferase as a promising therapeutic target for human African trypanosomiasis...
  14. ncbi Protein kinase inhibition of clinically important staurosporine analogues
    Osman A B S M Gani
    The Norwegian Structural Biology Center, Institute of Chemistry, University of Tromsø, 9037, Tromsø, Norway
    Nat Prod Rep 27:489-98. 2010
    ..Further, the mix of purely natural, biosynthetically and chemically modified compounds described here offer insights into prospects and strategies for drug discovery via bioprospecting...
  15. ncbi Impaired multimerization of human adiponectin mutants associated with diabetes. Molecular structure and multimer formation of adiponectin
    Hironori Waki
    Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, 113 8655, Japan
    J Biol Chem 278:40352-63. 2003
    ..In conclusion, not only total concentrations, but also multimer distribution should always be considered in the interpretation of plasma adiponectin levels in health as well as various disease states...
  16. ncbi Chemistry and biology of siderophores
    Robert C Hider
    Division of Pharmaceutical Science, King s College, London, SE1 9NH, UK
    Nat Prod Rep 27:637-57. 2010
    ..Clinically important siderophores and the therapeutic potential of siderophore design are described. Appendix 1 provides a comprehensive list of siderophore structures...
  17. ncbi Lobocrasol, a new diterpenoid from the soft coral Lobophytum crassum
    Shih Tseng Lin
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan
    Org Lett 11:3012-4. 2009
    ..Lobocrasol (1), possessing an unprecedented diterpenoid skeleton, was isolated from the soft coral Lobophytum crassum. The structure of lobocrasol was established by extensive analysis of spectroscopic data...
  18. pmc A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling
    Zachary A Knight
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
    Cell 125:733-47. 2006
    ..These results illustrate systematic target validation using a matrix of inhibitors that span a protein family...
  19. ncbi AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    R A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, UK
    J Biomol NMR 8:477-86. 1996
    ..They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results...
  20. pmc A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres
    Raphaël Rodriguez
    The University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
    J Am Chem Soc 130:15758-9. 2008
    ..We also show that the small molecule G-quadruplex binder induces a partial alteration of shelterin through POT1 uncapping from telomeres in human HT1080 cancer cells and the presence of gammaH2AX foci colocalized at telomeres...
  21. ncbi Human response to dioxin: aryl hydrocarbon receptor (AhR) molecular structure, function, and dose-response data for enzyme induction indicate an impaired human AhR
    Kevin T Connor
    Geomatrix, Inc, Folsom, California, USA
    J Toxicol Environ Health B Crit Rev 9:147-71. 2006
    ..response to binding of TCDD and related compounds to the AhR are consistent with the binding affinity and molecular structure data and support the hypothesis that the human AhR is less functional than the AhR of the more sensitive ..
  22. ncbi Creating new fluorescent probes for cell biology
    Jin Zhang
    Department of Pharmacology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 18 496, Cambridge, Massachusetts 02139, USA
    Nat Rev Mol Cell Biol 3:906-18. 2002
    ....
  23. ncbi Discovery and characterization of small molecule inhibitors of the BET family bromodomains
    Chun wa Chung
    Molecular Discovery Research, GlaxoSmithKline R and D, Stevenage SG5 4HT, UK
    J Med Chem 54:3827-38. 2011
    ..X-ray crystal structures of compounds bound into bromodomains of Brd2 and Brd4 elucidate the molecular interactions of binding and explain the precisely defined stereochemistry required for activity...
  24. ncbi Intramolecular hydrogen bonding in medicinal chemistry
    Bernd Kuhn
    Discovery Chemistry, F Hoffmann La Roche AG, CH 4070 Basel, Switzerland
    J Med Chem 53:2601-11. 2010
    The formation of intramolecular hydrogen bonds has a very pronounced effect on molecular structure and properties...
  25. ncbi Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    Renxiao Wang
    Medical Chemistry and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109 0934, USA
    J Comput Aided Mol Des 16:11-26. 2002
    ..Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking...
  26. ncbi Assessing the performance of OMEGA with respect to retrieving bioactive conformations
    Jonas Boström
    Department of Medicinal Chemistry, AstraZeneca R and D Molndal, S 431 83 Molndal, Sweden
    J Mol Graph Model 21:449-62. 2003
    ..Both databases provided satisfactory results in terms of retrieval. ROCS was able to rank 35 out of 36 X-ray structures among the top 500 hits from the large database...
  27. pmc Follow the leader: the use of leader peptides to guide natural product biosynthesis
    Trent J Oman
    Department of Chemistry, Howard Hughes Medical Institute, and Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
    Nat Chem Biol 6:9-18. 2010
    ....
  28. pmc The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2)
    Jonathan A Winger
    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, USA
    BMC Struct Biol 9:7. 2009
    ..Recent screens carried out to find off-target proteins that bind to imatinib identified the oxidoreductase NQO2, a flavoprotein that is phosphorylated in a chronic myelogenous leukemia cell line...
  29. pmc Stereochemical assignment, antiinflammatory properties, and receptor for the omega-3 lipid mediator resolvin E1
    Makoto Arita
    Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    J Exp Med 201:713-22. 2005
    ..These results demonstrate novel counterregulatory responses in inflammation initiated via RvE1 receptor activation that provide the first evidence for EPA-derived potent endogenous agonists of antiinflammation...
  30. pmc Interaction of HapX with the CCAAT-binding complex--a novel mechanism of gene regulation by iron
    Peter Hortschansky
    Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology HKI, and Friedrich Schiller University Jena, Jena, Germany
    EMBO J 26:3157-68. 2007
    ..Remarkably, CBC-mediated regulation has an inverse impact on the expression of the same gene set in A. nidulans, compared with Saccharomyces cerevisae...
  31. ncbi Structural and quantitative analysis of N-linked glycans by matrix-assisted laser desorption ionization and negative ion nanospray mass spectrometry
    David J Harvey
    Oxford Glycobiology Institute, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK
    Anal Biochem 376:44-60. 2008
    ..Quantities of glycans were measured by ESI and by matrix-assisted laser desorption ionization mass spectrometry; each technique produced virtually identical results for the neutral desialylated glycans...
  32. ncbi Molecular structure and physiological functions of GABA(B) receptors
    Bernhard Bettler
    Pharmazentrum, Dept of Clinical Biological Sciences, Institute of Physiology, Univ of Basel, Klingelbergstr 50, CH 4056 Basel, Switzerland
    Physiol Rev 84:835-67. 2004
    ..Here we review current concepts on the molecular composition and function of GABA(B) receptors and discuss ongoing drug-discovery efforts...
  33. pmc KEGG for linking genomes to life and the environment
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
    Nucleic Acids Res 36:D480-4. 2008
    ..KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers...
  34. pmc MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Nucleic Acids Res 32:W615-9. 2004
    ..This service is available free to all users at http://kinemage.biochem.duke.edu...
  35. ncbi Scientific basis for the therapeutic use of Withania somnifera (ashwagandha): a review
    L C Mishra
    Los Angeles College of Chiropractic LACC, 16200 E Amber Valley Dr, Whittier, CA 90609 1166
    Altern Med Rev 5:334-46. 2000
    ..Specifically, the literature was reviewed for articles pertaining to chemical properties, therapeutic benefits, and toxicity...
  36. ncbi Anti-inflammatory cembranoids from the soft corals Sinularia querciformis and Sinularia granosa
    Yi Lu
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 71:1754-9. 2008
    ..However, compounds 3, 7, and 8 significantly inhibited the accumulation of the pro-inflammatory iNOS and COX-2 proteins in LPS-stimulated RAW264.7 macrophage cells...
  37. ncbi Intermediate filaments: molecular structure, assembly mechanism, and integration into functionally distinct intracellular Scaffolds
    Harald Herrmann
    Department of Cell Biology, German Cancer Research Center, D 69120 Heidelberg, Germany
    Annu Rev Biochem 73:749-89. 2004
    ..Recent structural work has now begun to shed some light onto the complex fine tuning of structure and function in these fibrous, coiled coil forming multidomain proteins and their contribution to cellular physiology and gene regulation...
  38. pmc Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    Lily S Cheng
    National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093, USA
    J Med Chem 51:3878-94. 2008
    ..This ensemble-based VS and RCS approach may offer improvement over existing strategies for structure-based drug discovery...
  39. pmc Molecular dynamics: survey of methods for simulating the activity of proteins
    Stewart A Adcock
    NSF Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093 0365, USA
    Chem Rev 106:1589-615. 2006
  40. pmc Novel aromatase inhibitors by structure-guided design
    Debashis Ghosh
    Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
    J Med Chem 55:8464-76. 2012
    ..The observed structure-activity relationship is borne out by the X-ray data. Structure-guided design permits utilization of the aromatase-specific interactions for the development of next generation AIs...
  41. ncbi The hederagenin saponin SMG-1 is a natural FMLP receptor inhibitor that suppresses human neutrophil activation
    Tsong Long Hwang
    Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan
    Biochem Pharmacol 80:1190-200. 2010
    ..Taken together, our results demonstrate that SMG-1 is a natural inhibitor of the FMLP receptor, which may have the potential to be developed into a useful new therapeutic agent for treating neutrophilic inflammatory diseases...
  42. pmc Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit
    Paul V Fish
    Pfizer Worldwide Medicinal Chemistry, Pfizer Worldwide R and D, Ramsgate Road, Sandwich CT13 9NJ, United Kingdom
    J Med Chem 55:9831-7. 2012
    ..This has yielded a potent, selective compound with cell-based activity (PFI-1) that may further add to the understanding of BET family function within the bromodomains...
  43. ncbi NMR: prediction of molecular alignment from structure using the PALES software
    Markus Zweckstetter
    Department for NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
    Nat Protoc 3:679-90. 2008
    ..developed methods to predict a molecular alignment tensor and thus residual dipolar couplings for a given molecular structure. This provides many new opportunities for the study of the structure and dynamics of proteins, nucleic ..
  44. pmc 3,5-dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands
    David S Hewings
    Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U K
    J Med Chem 54:6761-70. 2011
    ..These compounds are promising leads for the further development of selective probes for the bromodomain and extra C-terminal domain (BET) family and CREBBP bromodomains...
  45. pmc Pyridostatin analogues promote telomere dysfunction and long-term growth inhibition in human cancer cells
    Sebastian Müller
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
    Org Biomol Chem 10:6537-46. 2012
    ..Our data emphasize the potential of a senescence-mediated anticancer therapy through the use of G-quadruplex targeting small molecules based on the molecular framework of pyridostatin...
  46. ncbi Manaarenolides A-I, diterpenoids from the soft coral Sinularia manaarensis
    Jui Hsin Su
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 69:1134-9. 2006
    ..The biosynthetic relationship between these new metabolites and 10 and 11 is also discussed...
  47. pmc Activation of lipoxin A(4) receptors by aspirin-triggered lipoxins and select peptides evokes ligand-specific responses in inflammation
    N Chiang
    Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    J Exp Med 191:1197-208. 2000
    ....
  48. ncbi Rapid assembly and in situ screening of bidentate inhibitors of protein tyrosine phosphatases
    Rajavel Srinivasan
    Department of Chemistry, Medicinal Chemistry Program of the Office of Life Sciences, National University of Singapore, 3 Science Drive 3, Singapore 117543, Republic of Singapore
    Org Lett 8:713-6. 2006
    ..Subsequent in situ enzymatic screening revealed a potential PTP1B inhibitor (IC(50) = 4.7 microM) which is 10-100 fold more potent than other PTPs...
  49. ncbi VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs
    Alessandro Pedretti
    Istituto di Chimica Farmaceutica e Tossicologica, University of Milan, Italy
    J Mol Graph Model 21:47-9. 2002
    ..The executable and the source code can be free downloaded from [URL: see text]...
  50. pmc Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents
    Marvin J Miller
    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
    Biometals 22:61-75. 2009
    ..Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described...
  51. pmc Small-molecule inhibitors target Escherichia coli amyloid biogenesis and biofilm formation
    Lynette Cegelski
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Chem Biol 5:913-9. 2009
    ..Thus, the ability of FN075 to block the biogenesis of both curli and type 1 pili endows unique anti-biofilm and anti-virulence activities on these compounds...
  52. pmc Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria
    Joshua A V Blodgett
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:11692-7. 2010
    ..These results establish the prevalence of frontalamide-like gene clusters in diverse bacterial types, with medicinally important Streptomyces species being particularly enriched...
  53. ncbi A comprehensive classification system for lipids
    Eoin Fahy
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0505, USA
    J Lipid Res 46:839-61. 2005
    ..This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases...
  54. ncbi Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    I Bahar
    Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
    Fold Des 2:173-81. 1997
    ..The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations...
  55. pmc High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy
    Christopher P Jaroniec
    Department of Chemistry and Center for Magnetic Resonance, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 101:711-6. 2004
    ..These findings provide an explanation of the unusual stability and characteristic properties of this form of polypeptide assembly...
  56. ncbi Marine natural products
    John W Blunt
    Department of Chemistry, University of Canterbury, Christchurch, New Zealand
    Nat Prod Rep 21:1-49. 2004
    ..Syntheses that lead to the revision of structures or stereochemistries have been included (114), including any first total syntheses of a marine natural product...
  57. pmc Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria
    Jerome S Pinkner
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:17897-902. 2006
    ..These pilicides thus target key virulence factors in pathogenic bacteria and represent a promising proof of concept for developing drugs that function by targeting virulence factors...
  58. ncbi Molecular structure of the Mycobacterium tuberculosis virulence factor, mycolic acid, determines the elicited inflammatory pattern
    Seppe Vander Beken
    Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
    Eur J Immunol 41:450-60. 2011
    ..tuberculosis to steer host immune responses during infection...
  59. ncbi Fragment-based discovery of bromodomain inhibitors part 1: inhibitor binding modes and implications for lead discovery
    Chun wa Chung
    Computational and Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R and D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
    J Med Chem 55:576-86. 2012
    ..An important implication is that the bromodomains are not only a phylogenetic family but also a system in which chemical and structural knowledge of one bromodomain gives insights transferrable to others...
  60. ncbi Fragment-based discovery of bromodomain inhibitors part 2: optimization of phenylisoxazole sulfonamides
    Paul Bamborough
    Epinova DPU, Immuno Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline R and D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
    J Med Chem 55:587-96. 2012
    ..This proof-of-principle experiment demonstrates the tractability of the BET family and bromodomain target class to fragment-based hit discovery and structure-based lead optimization...
  61. pmc Tetrazine ligation: fast bioconjugation based on inverse-electron-demand Diels-Alder reactivity
    Melissa L Blackman
    Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Am Chem Soc 130:13518-9. 2008
    ..The rate of the ligation between trans-cyclooctene and 3,6-di-(2-pyridyl)-s-tetrazine is very rapid (k2 2000 M-1 s-1). This fast reactivity enables protein modification at low concentration...
  62. ncbi Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species
    Irene de Bruijn
    Laboratory of Phytopathology, Wageningen University, 6709 PD Wageningen, The Netherlands
    Mol Microbiol 63:417-28. 2007
    ..The results indicate that genome mining may enable the discovery of unknown gene clusters and traits that are highly relevant in the lifestyle of plant beneficial and plant pathogenic bacteria...
  63. ncbi Relationships between molecular structure and perceived odor quality of ligands for a human olfactory receptor
    Guenhael Sanz
    Institut National de la Recherche Agronomique, Unité Minte de Recherche 1197 Neurobiologie de l Olfaction et de la Prise Alimentaire, F 78352 Jouy en Josas, France
    Chem Senses 33:639-53. 2008
    ..We demonstrated that OR1G1 recognizes a group of odorants that share both 3D structural and perceptual qualities. We hypothesized that OR1G1 contributes to the coding of waxy, fatty, and rose odors in humans...
  64. ncbi Pilicides-small molecules targeting bacterial virulence
    Veronica Aberg
    Department of Chemistry, Umea University, SE 90187, Umea, Sweden
    Org Biomol Chem 5:1827-34. 2007
    ..Pili are primarily involved in bacterial adhesion, invasion and persistence to host defenses. On this basis, pilicides can aid the development of new antibacterial agents...
  65. ncbi Structure validation by Calpha geometry: phi,psi and Cbeta deviation
    Simon C Lovell
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 50:437-50. 2003
    ..To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage)...
  66. ncbi Evolving trends in the dereplication of natural product extracts: new methodology for rapid, small-scale investigation of natural product extracts
    Gerhard Lang
    Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
    J Nat Prod 71:1595-9. 2008
    ..In each case the dereplication steps were carried out on microgram quantities of extract and demonstrate the discriminating power of (1)H NMR spectroscopy as a definitive dereplication tool...
  67. ncbi Matched molecular pairs as a guide in the optimization of pharmaceutical properties; a study of aqueous solubility, plasma protein binding and oral exposure
    Andrew G Leach
    AstraZeneca Pharmaceuticals, Mereside, Alderley Park, Macclesfield SK10 4TG, UK
    J Med Chem 49:6672-82. 2006
    ..In this paper, we focus upon the effects on aqueous solubility, plasma protein binding and oral exposure of adding substituents to aromatic rings and methylating heteroatoms...
  68. ncbi A novel fluorescent probe for the detection of nitric oxide in vitro and in vivo
    Jie Ouyang
    The School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300191, China
    Free Radic Biol Med 45:1426-36. 2008
    ..The results demonstrate that MNIP-Cu can act as a novel fluorescent probe for nitric oxide and has many potential applications in biomedical research...
  69. ncbi Docking study yields four novel inhibitors of the protooncogene Pim-1 kinase
    Albert C Pierce
    Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA
    J Med Chem 51:1972-5. 2008
    ..091 and 4.5 microM. This gives a 14-fold enrichment over the earlier HTS run, and the two crystal structures solved confirmed the binding modes predicted by docking...
  70. doi Copper-mediated coupling reactions and their applications in natural products and designed biomolecules synthesis
    Gwilherm Evano
    Institut Lavoisier de Versailles, UMR CNRS 8180, Universite de Versailles Saint Quentin en Yvelines, 45 Avenue des Etats Unis, 78035 Versailles Cedex, France
    Chem Rev 108:3054-131. 2008
  71. ncbi Profiles and levels of fatty acid esters of okadaic acid group toxins and pectenotoxins during toxin depuration. Part II: blue mussels (Mytilus edulis) and flat oyster (Ostrea edulis)
    Trine Torgersen
    National Veterinary Institute, Department of Feed and Food Safety, P O Box 750 Sentrum, NO 0106 Oslo, Norway
    Toxicon 52:418-27. 2008
    ..Hence, although produced by the same Dinophysis species, conclusions about the dynamics of one toxin group based on results from the other group should be avoided in future studies...
  72. ncbi Inhibition of cell proliferation by quindoline derivative (SYUIQ-05) through its preferential interaction with c-myc promoter G-quadruplex
    Tian Miao Ou
    School of Pharmaceutical Sciences, Sun Yat Sen University, Guangzhou University City, Waihuan East Road 132, Guangzhou 510006, People s Republic of China
    J Med Chem 54:5671-9. 2011
    ..Therefore, it is possible that this compound had its antitumor activity for cancer cells mainly through its interaction with c-myc quadruplex...
  73. ncbi Structural insights into how irreversible inhibitors can overcome drug resistance in EGFR
    Anja Michalczyk
    Chemical Genomics Centre of the Max Planck Society, Otto Hahn Strasse 15, 44227 Dortmund, Germany
    Bioorg Med Chem 16:3482-8. 2008
    ..This 4-(phenylamino)quinazoline inhibits wild type and drug resistant EGFR in vitro at low nM concentrations. The co-crystal structure of drug resistant cSrc-T338M kinase domain provides the structural basis of this activity...
  74. pmc Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis
    Holger Jenke-Kodama
    Department of Molecular Ecology, Institute of Biology, Humboldt University, Berlin, Germany
    PLoS Comput Biol 2:e132. 2006
    ..Our results indicate that homologous recombination facilitated by the modularity of PKS architecture is the most important mechanism underlying polyketide diversity in bacteria...
  75. ncbi Loline alkaloids: Currencies of mutualism
    Christopher L Schardl
    Department of Plant Pathology, 201F Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546 0312, USA
    Phytochemistry 68:980-96. 2007
    ....
  76. pmc NCI: A server to identify non-canonical interactions in protein structures
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 31:3345-8. 2003
    ..In addition, the user can view the RasMol image highlighting the interactions in the protein structure and download the RasMol script. The NCI server is available at: http://www.mrc-lmb.cam.ac.uk/genomes/nci/...
  77. pmc Hybrid peptide dendrimers for imaging of chemokine receptor 4 (CXCR4) expression
    Joeri Kuil
    Division of Diagnostic Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands
    Mol Pharm 8:2444-53. 2011
    ..Thus, multimerization of the cyclic Ac-TZ14011 peptide reduces the negative influence of the multimodal label on the receptor affinity and the biodistribution...
  78. ncbi 1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus
    A Carfi
    LCM, Institut de Biologie Structurale Jean Pierre Ebel CEA CNRS, Grenoble, France
    Acta Crystallogr D Biol Crystallogr 54:313-23. 1998
    ..In addition, the structure of the apo enzyme was determined at 2.5 A resolution. The removal of the zinc ion by chelating agents causes small changes in the active-site environment...
  79. ncbi Principles and applications of halogen bonding in medicinal chemistry and chemical biology
    Rainer Wilcken
    Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
    J Med Chem 56:1363-88. 2013
    ..In light of these data, we discuss the potential and limitations of exploiting halogen bonds for molecular recognition and rational drug design. ..
  80. ncbi Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase DprE1
    Claudia Trefzer
    More Medicines for Tuberculosis MM4TB Consortium, and Institute of Chemical Sciences and Engineering, NCCR Chemical Biology, École Polytechnique Fédérale de Lausanne EPFL, Lausanne, Switzerland
    J Am Chem Soc 134:912-5. 2012
    ..Our results explain the basis for drug sensitivity and resistance to an exceptionally potent class of antituberculosis agents...
  81. pmc Bioactive natural products from Lysobacter
    Yunxuan Xie
    Department of Chemistry, University of Nebraska Lincoln, NE 68588, USA
    Nat Prod Rep 29:1277-87. 2012
    ..We hope to provide a snapshot of the important work done on the lysobacterial natural products and to provide useful information for future biosynthetic engineering of novel antibiotics in Lysobacter...
  82. ncbi Monomer composition and sequence of alginates from Pseudomonas aeruginosa
    N Schürks
    Institut fur Chemie, Universität Duisburg, 47048 Duisburg, Germany
    Int J Biol Macromol 30:105-11. 2002
    ..The strong preference for MG-pairs in the parent strain of P. aeruginosa may be connected to a stronger binding of cations in the MG-vicinity...
  83. ncbi A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes
    Helene Köster
    Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
    J Med Chem 54:7784-96. 2011
    ..They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes...
  84. ncbi Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes
    Nancy H Campbell
    CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, 29 29 Brunswick Square, London WC1N 1AX, U K
    J Med Chem 55:209-22. 2012
    ..The complexes show significant antiproliferative activity for the compounds in a panel of cancer cell lines. They also show telomerase inhibitory activity in the telomerase TRAP-LIG assay...
  85. ncbi Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein
    G M Preston
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
    Science 256:385-7. 1992
    ..Although selective for water, the molecular structure of these channels is unknown...
  86. ncbi Archaebacterial bipolar tetraether lipids: Physico-chemical and membrane properties
    Parkson Lee Gau Chong
    Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140, United States
    Chem Phys Lipids 163:253-65. 2010
    ..Special attention of this article is focused on how the number of cyclopentane rings varies with environmental factors and affects membrane properties...
  87. ncbi Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks
    Francisco J Prado-Prado
    Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
    Bioorg Med Chem 17:569-75. 2009
    ..We also give the procedure for the construction of Back-Projection Maps for the contribution of each drug sub-structure to the antiviral activity against different species...
  88. ncbi The chemistry and applications of antimicrobial polymers: a state-of-the-art review
    El Refaie Kenawy
    Department of Chemistry, Polymer Research Group, Faculty of Science, University of Tanta, Tanta 31527, Egypt
    Biomacromolecules 8:1359-84. 2007
    ....
  89. pmc A sesquiterpene quinone, dysidine, from the sponge Dysidea villosa, activates the insulin pathway through inhibition of PTPases
    Yu Zhang
    Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
    Acta Pharmacol Sin 30:333-45. 2009
    ..In order to probe the potential anti-diabetic effect of the sesquiterpene hydroquinones/quinones, the effect of dysidine on the insulin pathway was studied...
  90. ncbi Alkaloids from the bark of Guatteria hispida and their evaluation as antioxidant and antimicrobial agents
    Emmanoel Vilaça Costa
    Departamento de Quimica, Universidade Federal de Sergipe, Avenida Marechal Rondon, S N, Rosa Elze, 49100 000, Sao Cristovao, SE, Brazil
    J Nat Prod 73:1180-3. 2010
    ..The major compounds, 2, 6, 12, and 13, showed significant antioxidant capacity in the ORAC(FL) assay. Compounds 5, 6, and 7 were active against S. epidermidis and C. dubliniensis, with MIC values in the range 12.5-100 microg mL(-1)...
  91. ncbi Palladium-catalyzed oxidative carbocyclization/arylation of enallenes
    Tuo Jiang
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE 10691, Stockholm, Sweden
    Org Lett 13:5838-41. 2011
    ..The reaction shows wide tolerance toward highly functionalized arylboronic acids and results in a cis addition of two carbon moieties to an olefin in good to excellent yields...
  92. ncbi Identification and characterization of a novel vitamin B12 (cobalamin) biosynthetic enzyme (CobZ) from Rhodobacter capsulatus, containing flavin, heme, and Fe-S cofactors
    Helen M McGoldrick
    School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
    J Biol Chem 280:1086-94. 2005
    ..A mechanism for Orf663 (CobZ) in cobalamin biosynthesis is proposed...
  93. ncbi VolSurf: a new tool for the pharmacokinetic optimization of lead compounds
    G Cruciani
    Laboratory for Chemometrics, University of Perugia, Via Elce di Sotto 10, I 06123 Perugia, Italy
    Eur J Pharm Sci 11:S29-39. 2000
    ..The method thus appears as a valuable new property filter in virtual screening and as a novel tool in optimizing the pharmacokinetic profile of pharmaceutically relevant compounds...
  94. ncbi Efficient activation of p53 pathway in A549 cells exposed to L2, a novel compound targeting p53-MDM2 interaction
    Lei Zhang
    Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
    Anticancer Drugs 20:416-24. 2009
    ..The changes of p53 and MDM2 protein levels in L2-treated HL60 cells indicated that the mechanisms involved in the cell cycle arrest in A549 and HL60 cells were probably different, to which our future research would be devoted...
  95. ncbi New fluorescent rhodamine hydrazone chemosensor for Cu(II) with high selectivity and sensitivity
    Yu Xiang
    Department of Chemistry, Tsinghua University, Beijing, PR China
    Org Lett 8:2863-6. 2006
    ..Upon the addition of Cu(II), the spirolactam ring of 1 was opened and a 1:1 metal-ligand complex was formed. The detection of Cu(II) by 1 at a lower micromolar level was successful even in buffered water...
  96. pmc A novel approach for predicting P-glycoprotein (ABCB1) inhibition using molecular interaction fields
    Fabio Broccatelli
    Laboratory of Chemometrics, Department of Chemistry, University of Perugia, Via Elce di Sotto 10, I 06123 Perugia, Italy
    J Med Chem 54:1740-51. 2011
    ..All of the validations confirmed the robustness of the model and its suitability to help medicinal chemists in drug discovery. The information derived from the model was rationalized as a pharmacophore for competitive Pgp inhibition...
  97. ncbi Lipid mediator class switching during acute inflammation: signals in resolution
    B D Levy
    Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
    Nat Immunol 2:612-9. 2001
    ....
  98. ncbi Meroditerpenoids from a Formosan soft coral Nephthea chabrolii
    Jui Hsin Su
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung 804, Taiwan, Republic of China
    J Nat Prod 68:1651-5. 2005
    ..Cytotoxic activity of metabolites 1-3 and 5-8 against a limited panel of cancer cell lines is also described...
  99. ncbi New 19-oxygenated and 4-methylated steroids from the Formosan soft coral Nephthea chabroli
    Shi Yie Cheng
    Department of Marine Biotechnology and Resources, National Sun Yat Sen University, Kaohsiung, Taiwan
    Steroids 74:543-7. 2009
    ..Compounds 1-5 were evaluated for anti-inflammatory activity using RAW 264.7 macrophages...
  100. ncbi Delineating mechanisms of dissociation for isomeric heparin disaccharides using isotope labeling and ion trap tandem mass spectrometry
    Ola M Saad
    Department of Chemistry, University of California at Berkeley, Berkeley, California 94720 1460, USA
    J Am Soc Mass Spectrom 15:1274-86. 2004
    ....
  101. ncbi Deep-sea natural products
    Danielle Skropeta
    School of Chemistry, University of Wollongong, Wollongong, Australia
    Nat Prod Rep 25:1131-66. 2008
    ..Relevant synthetic studies on the deep-sea natural products have also been included...

Research Grants68

  1. Computer/Electrical Engineering
    Theodore Raphan; Fiscal Year: 2011
    ..This would make analysis of molecular structure more accessible to individual investigators. D...
  2. Analogs of GTP as novel inhibitors of bacterial c-di-GMP-synthesizing enzymes
    George E Wright; Fiscal Year: 2010
    ..e. where a modified c-di-GMP has been produced, LCMS will be used to quantitate and determine the molecular structure of the product(s);and 3, selectively test potent inhibitors for effects on c-di-GMP production and biofilm ..
  3. Multiplexed DNA Origami-Based Biomarker Detection Assay for Early Dx of Arthritis
    John E Mueller; Fiscal Year: 2013
    ..AIM 3: Identify and characterize DNA origami molecules that bind the AR biomarkers. Due to the DNA origami molecular structure, the interaction between these molecules and the AR biomarkers should exhibit increased binding affinities, ..
  4. Moraxella catarrhalis: virulence-based prevention
    Timothy F Murphy; Fiscal Year: 2013
    ..In Aim 2 we will elucidate the molecular structure of OppA and related transporters in the bacterial cell wall to identify potentially protective epitopes and ..
  5. Chromatin regulation by human SIRT7 in aging-associated cellular programs
    Katrin F Chua; Fiscal Year: 2013
    ..on aging- and cancer- associated cellular programs through a novel biochemical activity at chromatin, the molecular structure in which the DNA of mammalian genomes is packaged...
  6. STRUCTURE OF THE VACUOLAR ATPase
    Stephan Wilkens; Fiscal Year: 2013
    ..The Specific Aims of the now proposed work on the vacuolar ATPase are: (1) molecular structure and function of the vacuolar ATPase proton channel domain and (2) molecular structure and function of the ..
  7. Gene Regulation by and of LEDGF
    Dhirendra P Singh; Fiscal Year: 2012
    ..Despite the known regulatory function of LEDGF, only limited investigation has been made into the molecular structure-function relationship of LEDGF's domains...
  8. Investigation of the structure and function of urea amidolyase
    MARTIN RAOUL ST. MAURICE; Fiscal Year: 2012
    ..This project will use protein X-ray crystallography to determine the molecular structure of the enzyme active sites of UAL and will combine crystallography with protein engineering and steady-..
  9. MOLECULAR BASIS OF INHERITED DEAFNESS
    David P Corey; Fiscal Year: 2013
    ..The molecular structure of the bond between cadherin 23 and protocadherin 15 suggested by these studies will be tested by ..
  10. Oligosaccharide moieties of human milk glycans that inhibit pathogens
    David S Newburg; Fiscal Year: 2013
    ..analytical techniques that have recently become available and can provide detailed understanding of the molecular structure of complex glycan moieties...
  11. FUNCTION OF THE KINETOPLAST IN THE HEMOFLAGELLATES
    Larry Simpson; Fiscal Year: 2013
    ..protein-protein and protein-RNA interactions in different functional states of the editing reaction The molecular structure information will be interpreted in terms of the detailed mechanism of this pathway and this knowledge will ..
  12. STUDIES ON THE STRUCTURE OF BASEMENT MEMBRANES
    BILLY GERALD HUDSON; Fiscal Year: 2013
    ..Aim 5: To determine the molecular structure of complete GP neoepitopes in the 13NC1 monomer...
  13. Structural Rearrangements in GABA-A Receptors
    CYNTHIA M CZAJKOWSKI; Fiscal Year: 2012
    ..The long-term goal of our research program is to understand the function of the GABAAR in terms of its molecular structure. While recent crystallographic advances have provided valuable structural models of the GABAAR, achieving a ..
  14. M tuberculosis Membrane Protein Pharmaceutical Targets
    Timothy A Cross; Fiscal Year: 2013
    ..Assays coupled with molecular structure will help establish structure-activity-relationships...
  15. DNA cross-linking by diepoxybutane
    Natalia Y Tretyakova; Fiscal Year: 2013
    ..The presence of two oxirane groups within the molecular structure of DEB allows it to form DNA-DNA cross-links by consecutively alkylating two adjacent nucleobases in a DNA ..
  16. Interatction of Estrogen, Age and Activity on Musculoskeletal Strength in Females
    Dawn A Lowe; Fiscal Year: 2013
    ..performance, maximal in vivo lower-leg muscle strength, contractile capacity of isolated muscles, and molecular structure-function analyses of myosin...
  17. Cancer cell signaling through lipids complexed to proteins
    RAYMOND DANIEL BLIND; Fiscal Year: 2013
    ..improvements of these inhibitors and training the PI in crystallography, X-ray diffraction methods and molecular structure determination, taking advantage of a relatively low-risk project...
  18. Elderly Immune Response to Pneumococcal Polysaccharide
    M A JULIA WESTERINK; Fiscal Year: 2010
    ..An increased understanding of the relationship between anti-PPS antibody molecular structure and protective capacity would greatly benefit future pneumococcal vaccine and adjuvant design...
  19. Skin Homing T Cells -- Molecular Characterization of CLA
    Thomas S Kupper; Fiscal Year: 2012
    ..provided by applicant): In the first two funding cycles of this grant, we have characterized the molecular structure and function of Cutaneous Lymphocyte Antigen or CLA...
  20. X-RAY AND CHEMICAL STUDIES OF METALLOPORPHYRINS
    W Robert Scheidt; Fiscal Year: 2010
    ..The approach utilizes the determination of molecular structure, typically by X-ray diffraction, and relating detailed structural features to other measured properties, ..
  21. Mechanotransduction Approach to Improve Bone Quality in Osteogenesis Imperfecta
    Charlotte L Phillips; Fiscal Year: 2012
    ..bearing) exercise regimens will increase muscle contractile generating capacity and endurance, alter the molecular structure of bone mineral and matrix, and improve bone physicochemical properties/biomechanical integrity in oim and ..
  22. Molecular pathogenesis of anti-glomerular basement membrane nephritis
    Dorin Bogdan Borza; Fiscal Year: 2012
    ..We hypothesize that the formation of pathogenic antibodies is determined by both molecular structure of the antigen and the host genetic background (antigen-deficient or -sufficient)...
  23. IMMUNE RESPONSE TO CRYPTOCOCCAL INFECTIONS
    STUART MICHAEL LEVITZ; Fiscal Year: 2012
    ..In an effort to develop a vaccine, the PI has identified the molecular structure of MP and explored the mechanisms by which MP stimulate T-cell responses...
  24. The Molecular Structure of the RNA Polymerase Portal of a Bacteriophage-Reovirus
    PAUL JEFFREY GOTTLIEB; Fiscal Year: 2013
    ..We anticipate that the optical qualities of viral proteins that we discover are applicable to human pathogens, in particular influenza. ..
  25. Biological roles of galectins
    GERARDO RAUL VASTA; Fiscal Year: 2013
    ..Several galectin types have been described (proto, chimera, and tandem-repeat), each endowed with a unique molecular structure, biochemical properties, and taxonomic distribution...
  26. Connecting plasma membrane function to lipid structure and organization with asym
    Noah Malmstadt; Fiscal Year: 2013
    ..The vast variety of molecular structure outside of the central dogma, particularly among lipids and carbohydrates, suggests that these, too, can be ..
  27. Fe porphyrin-based Redox Modulator in Experimental Stroke Outcome
    Ines Batinic-Haberle; Fiscal Year: 2013
    ..Due to different molecular structure, Fe porphyrin does not cause arterial hypotension in experimental animals, it is less toxic, and exerts ~2-..
  28. Structural origin of fibrin clot mechanical properties
    John W Weisel; Fiscal Year: 2012
    ..More generally, this research involves the determination of relationships between molecular structure and the mechanical properties of a remarkable biological material, the blood clot.
  29. Genomics of Cardiac Electrical Activity and Arrhythmia
    Nona Sotoodehnia; Fiscal Year: 2013
    ..regions may have a role in arrhythmias, it is clear that variants in exonic regions that change the molecular structure of a protein can lead to alteration in protein function and influence downstream phenotypes...
  30. Molecular Characterization of C. neoformans Antibodies
    Arturo Casadevall; Fiscal Year: 2013
    ..Three specific Aims are proposed: 1) To define the polysaccharide molecular structure(s) that bind protective and non-protective mAbs;2) To determine the mechanism and consequences of antibody-..
  31. A novel neuropeptide system involved in drug abuse
    Olivier Civelli; Fiscal Year: 2013
    ..This changed with our and others discovery of the molecular structure of MCH1 receptor (MCH1R), which propelled the MCH system at the forefront of anti obesity drug research...
  32. Glucose Modifications of Proteins in Diabetic Nephropathy
    BILLY GERALD HUDSON; Fiscal Year: 2013
    ..nuclear magnetic resonance spectroscopy, research technologies that can provide precise information about molecular structure of renal tissues...
  33. Spectroscopic Probes of the Muscle Cytoskeleton
    David D Thomas; Fiscal Year: 2013
    ..by applicant): Spectroscopic Probes of the Muscle Cytoskeleton Our long-term goal is to define the molecular structure and dynamics that determine the functions of dystrophin (Dys) and utrophin (Utr) in striated muscle, in ..
  34. Roles of class 1A PI3K isoforms in mammary epithelium function and breast cancer
    Jean Zhao; Fiscal Year: 2012
    ..Despite their similarity in molecular structure and enzymatic activity, recent studies suggest that the two isoforms have distinct functions in cell ..
  35. MOLECULAR CLONING OF EPITHELIAL K CHANNELS
    Henry Sackin; Fiscal Year: 2012
    ..are these two gates linked together at a structural level? Is external K gating of ROMK dependent on the molecular structure of the pH gate at the bundle crossing? Do changes in selectivity filter conformation constitute a second (C-..
  36. Mechanisms of fusion and transmitter release in neurosecretion
    Manfred Lindau; Fiscal Year: 2012
    ..This project is aimed at elucidating the molecular structure and dynamics of the fusion pore and mechanism by which transmitters are released through the fusion pore.
  37. Nitrosative stress defenses in periodontopathogen Porphyromonas gingivalis
    Janina P Lewis; Fiscal Year: 2013
    ..Furthermore, we will carry out molecular structure studies of HcpR and of its complexes with DNA using NMR and crystallography...
  38. Molecular Biology of the Odorant Receptors
    Leslie B Vosshall; Fiscal Year: 2011
    ..Responsive to PA-05-154, the overall goal of this specific project is to increase understanding of the molecular structure and function of the odorant receptors (ORs) that mediate odor recognition in insects...
  39. Structure and Function of NMDA Receptors
    Hiroyasu Furukawa; Fiscal Year: 2013
    ..Defining the molecular structure of the extracellular region of NMDA receptors is expected to help in the design of new therapeutics.
  40. STRUCTURAL ANALYSIS OF G PROTEIN REGULATORY MECHANISMS
    STEPHEN SPRANG; Fiscal Year: 2009
    ..respective roles in two different G protein-regulated cellular pathways will by elucidated at the level of molecular structure and dynamics...
  41. High resolution electron cryo-microscope at Brandeis University.
    Nikolaus Grigorieff; Fiscal Year: 2009
    ..The molecular structure of a number of morphologies of these fibrils will be determined by cryo-EM...
  42. Ultrafast Spectroscopic Methods to Probe Photodamage and Unfolding in Biopolymers
    David W McCamant; Fiscal Year: 2012
    ..In each of these cases, there are few experimental techniques that can resolve the dynamic molecular structure of the evolving system...
  43. Actions of Vif and APOBEC3 proteins in HIV-1 Replication
    Yong Hui Zheng; Fiscal Year: 2010
    ..This proposal will address three specific aims: (1) To study the molecular structure of this antiviral innate immunity and identify additional APOBEC3 family members;(2) To study the enzymatic ..
  44. New Leads Against Cancer and Infectious Diseases from Puerto Rican Reef Species
    Abimael D Rodriguez; Fiscal Year: 2013
    ..Further purification by chromatography (column, GC, LC) and determination of molecular structure will proceed if warranted by the screening results...
  45. Prediction of influenza antigenic variants using a novel sparse multitask learnin
    Xiu Feng Wan; Fiscal Year: 2010
    ..Enabling Technologies and fit for the Specific Challenge 06-GM-103: development of predictive method for molecular structure, recognition, and ligand interaction...
  46. Development of inhibitors of the calcium-activated chloride channel TMEM16a
    Marc O Anderson; Fiscal Year: 2013
    ..The central hypotheses of this proposal are: (a) the molecular structure of the 2-amino-4-arylthiazoles can be modified at several positions to alter the interactions with TMEM16A, ..
  47. Mechanisms of Intercelllar Communication
    VYTAUTAS K VERSELIS; Fiscal Year: 2013
    ..The objectives are to: 1) Provide outstanding postdoctoral training in basic research on molecular structure and physiological function of electrical and chemical synapses;2) Capitalize on the synergism and ..
  48. A. gambiae thioester-containing protein 1 (TEP1) protein-protein interactions
    Richard H G Baxter; Fiscal Year: 2011
    ..A fundamental understanding of molecular structure and protein-protein interactions involving TEP1 are necessary to understand how it kills malaria parasites...
  49. Modulation of Kir Channel Function by Phosphorylation
    Diomedes E Logothetis; Fiscal Year: 2012
    ..term goal of our laboratory in general is to understand ion channel function and regulation in terms of molecular structure and in particular to gain mechanistic insight for the dependence of Kir activity on PIP2...
  50. Immune Response to pneumococcal vaccination in HIV infected adults
    M A Westerink; Fiscal Year: 2009
    ..A comprehensive study, directly linking anti-PPS antibody levels, functionality and molecular structure/gene family usage, has not been performed...
  51. Tight Junction Barriers in the Gastrointestinal Tract
    James Melvin Anderson; Fiscal Year: 2010
    ..impediment to interpreting and correcting these pathologic changes is that we lack an understanding of the molecular structure of the barrier and the basis for its size- and charge- selectivity and permeability...
  52. Cardiac Myosin Binding Protein-C: Structure, Function, and Regulation
    David M Warshaw; Fiscal Year: 2013
    ..The Program Project's long term goals are to: 1) define cMyBP-C's molecular structure and sarcomeric organization;2) determine how cMyBP-C modulates cardiac function in a phosphorylation-..
  53. Age-Dependent Regulation of Excitation-Contraction Coupling
    Osvaldo Delbono; Fiscal Year: 2013
    ..A better understanding of the decline in skeletal muscle molecular structure and function will allow more rationale interventions aimed at improving physical performance and ..
  54. Structural bioinformatics software for epitope selection and antibody engineering
    STEVEN JOSEPH DARNELL; Fiscal Year: 2012
    ..The proposed software pipeline will be built upon Protean 3D, our new molecular structure and simulation viewer, and will elevate the technical capability of a broad range of experimental ..
  55. Membrane-targeting calcium sensors in vision
    James B Ames; Fiscal Year: 2013
    ..resonance (NMR) techniques and use them in concert with other experimental approaches to elucidate the molecular structure and physiologic functions of selected membrane-targeting proteins involved in phototransduction in vision ..
  56. MOLECULAR CHARACTERIZATION OF FIV
    John H Elder; Fiscal Year: 2013
    ..The proposed studies will further define the molecular structure and replication properties of FIV with particular emphasis on defining targets for development of broad-..
  57. Force spectroscopy platform for label free genome sequencing
    DMITRI VEZENOV; Fiscal Year: 2010
    ..detection of a single nucleotide addition (SNA) can be based on changes in mechanical properties and molecular structure of single DNA fragments...
  58. Mechanism of Potent Neutralization of HIV by IgA CD4i Antibody
    Lisa A Cavacini; Fiscal Year: 2013
    ..Therefore, we hypothesize that IgA isotypes of CD4i antibodies through their unique molecular structure can increase the neutralizing activity against HIV infection...
  59. MULTIPARAMETRIC MRI OF CARTILAGE
    Deborah Burstein; Fiscal Year: 2009
    ..and specificity to GAG;T2 imaging of cartilage is based on the sensitivity of T2 to hydration, collagen molecular structure, and collagen architectural organization through the magic angle effect;diffusion has been shown to ..
  60. Co(II)-Radical Pair Dynamics in B12 Enzyme Catalysis
    Kurt Warncke; Fiscal Year: 2012
    ..The contributions of molecular structure and dynamics to enzyme function will be studied by using techniques of pulsed-electron paramagnetic ..
  61. REGULATION OF CYCLIC GMP SYNTHESIS IN PHOTORECEPTORS
    Alexander M Dizhoor; Fiscal Year: 2013
    ..Aim 1 will address the molecular structure of GCAP1 with the emphasis on establishing the key to the conformational transition of GCAP1 into its RetGC ..
  62. Texas A&M University Interdisciplinary Life Sciences Building Build-Out
    JEFFREY RANDALL SEEMANN; Fiscal Year: 2010
    ..and it is facilitated by harnessing the power of techniques like high-throughput drug screening and molecular structure determination...
  63. Investigation of protein interactions in intrinsic blood coagulation pathway
    Divi Venkateswarlu; Fiscal Year: 2007
    ..Thus, there is a great deal of interest in understanding the molecular structure of the three proteins VIIIa,IXa and FX and to develop a structure-function relationship among the three ..
  64. Superior Near-IR Dyes for Bioimaging
    ARUNKUMAR EASWARAN; Fiscal Year: 2009
    ..to improve dye performance by introducing water solublizing sulfonate or phosphonic acid groups into the molecular structure. With further development, they are likely to become superior replacements for the popular cyanine (Cy5) ..
  65. MOLECULAR STRUCTURE OF STEROIDS
    William Duax; Fiscal Year: 2001
    ..The Molecular Structure of Steroids Project has generated hundreds of steroid crystal structures in collaboration with biochemists, ..
  66. REGULATION OF INDUCIBLE RAT SALIVARY CYSTATIN
    Gurrinder Bedi; Fiscal Year: 1990
    ..proteinase inhibitors of the cystatin superfamily are grouped into three families on the basis of their molecular structure. Family 1 cystatins are found mainly intracellularly and are present as constituative components of many ..
  67. Electronic/Molecular Structure of Enzyme Heme Pockets
    GERD LA MAR; Fiscal Year: 2009
    ..Our interests focus on comparison of local solution with cryogenic crystallographic molecular structure, with particular attention paid to extended H-bond networks with some remarkably robust H-bonds, and the ..
  68. Intervention against anthrax edema factor (EF)
    Wei Jen Tang; Fiscal Year: 2005
    ..We have determined the molecular structure of EF alone and EF in complex with calmodulin to show that the interaction of EF with calmodulin is ..