Arash Bahrami

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. pmc Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy
    Arash Bahrami
    Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Comput Biol 5:e1000307. 2009
  2. ncbi request reprint HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections
    Gabriel Cornilescu
    National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, WI 53706, USA
    J Biomol NMR 38:341-51. 2007
  3. pmc Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers
    Woonghee Lee
    National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA Biochemistry Department, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA Electronic address
    J Magn Reson 236:83-8. 2013
  4. ncbi request reprint Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)
    Hamid R Eghbalnia
    Biochemistry Department, National Magnetic Resonance Facility at Madison, 433, Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:219-33. 2005
  5. pmc Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR
    Arash Bahrami
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS ONE 7:e33173. 2012
  6. pmc PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy
    Woonghee Lee
    National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin Madison, Madison, WI 53706, USA
    Bioinformatics 25:2085-7. 2009
  7. ncbi request reprint Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements
    Hamid R Eghbalnia
    Biochemistry Department, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:71-81. 2005
  8. pmc ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy
    Woonghee Lee
    National Magnetics Resonance Facility at Madison, University of Wisconsin Madison, Madison, WI 53706, USA
    Bioinformatics 29:515-7. 2013
  9. pmc RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts
    Arash Bahrami
    National Magnetic Resonance Facility at Madison, Madison, WI, USA
    J Biomol NMR 52:289-302. 2012
  10. ncbi request reprint High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection
    Hamid R Eghbalnia
    National Magnetic Resonance Facility at Madison, Center for Eukaryotic Structural Genomics, Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Am Chem Soc 127:12528-36. 2005

Collaborators

Detail Information

Publications13

  1. pmc Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy
    Arash Bahrami
    Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Comput Biol 5:e1000307. 2009
    ..PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination...
  2. ncbi request reprint HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections
    Gabriel Cornilescu
    National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, WI 53706, USA
    J Biomol NMR 38:341-51. 2007
    ..The statistical measure of reliability, measuring the quality of each RDC value, offers valuable adjunct information even in cases where modest time savings may be realized...
  3. pmc Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers
    Woonghee Lee
    National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA Biochemistry Department, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA Electronic address
    J Magn Reson 236:83-8. 2013
    ..ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use...
  4. ncbi request reprint Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)
    Hamid R Eghbalnia
    Biochemistry Department, National Magnetic Resonance Facility at Madison, 433, Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:219-33. 2005
    ..PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data...
  5. pmc Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR
    Arash Bahrami
    National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS ONE 7:e33173. 2012
    ..We present test cases in which ADAPT-NMR achieved results in two days or less that would have taken two months or more by manual approaches...
  6. pmc PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy
    Woonghee Lee
    National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin Madison, Madison, WI 53706, USA
    Bioinformatics 25:2085-7. 2009
    ..Once assignments are fixed, the output files generated by PINE-SPARKY can be used as input to PINE-NMR for further refinements...
  7. ncbi request reprint Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements
    Hamid R Eghbalnia
    Biochemistry Department, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:71-81. 2005
    ....
  8. pmc ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy
    Woonghee Lee
    National Magnetics Resonance Facility at Madison, University of Wisconsin Madison, Madison, WI 53706, USA
    Bioinformatics 29:515-7. 2013
    ..list) and TALOS+ input file (.tab). As an example, we show how ADAPT-NMR Enhancer was used to extend the automated data collection and assignment results for the protein Aedes aegypti sterol carrier protein 2...
  9. pmc RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts
    Arash Bahrami
    National Magnetic Resonance Facility at Madison, Madison, WI, USA
    J Biomol NMR 52:289-302. 2012
    ..RNA-PAIRS is available as a public web-server at http://pine.nmrfam.wisc.edu/RNA/...
  10. ncbi request reprint High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection
    Hamid R Eghbalnia
    National Magnetic Resonance Facility at Madison, Center for Eukaryotic Structural Genomics, Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    J Am Chem Soc 127:12528-36. 2005
    ..HIFI-NMR required about one-tenth the time for data collection and avoided subsequent data processing and peak-picking. The approach can be implemented on commercial NMR spectrometers and is extensible to higher-dimensional NMR...
  11. ncbi request reprint Resonance assignments for the two N-terminal RNA recognition motifs (RRM) of the S. cerevisiae pre-mRNA processing protein Prp24
    Nicholas J Reiter
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
    J Biomol NMR 36:58. 2006
  12. pmc Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1
    Shanteri Singh
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Protein Sci 14:2095-102. 2005
    ..This structural similarity bolsters the hypothesis that ubiquitin and ubiquitin-related proteins evolved from a protein-based sulfide donor system of the molybdopterin synthase type...
  13. ncbi request reprint Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications
    Liya Wang
    National Magnetic Resonance Facility at Madison, Biochemistry Department, 433 Babcock Drive, Madison, WI 53706, USA
    J Biomol NMR 32:13-22. 2005
    ..This database can serve as a resource for future analysis of the effects of amino acid sequence and protein secondary and tertiary structure on NMR chemical shifts...