th  - 1988 - 51st ENC Conference

9o j
THREE-DIMENS~ONAL STUCTURE DETERMINATION OF DNA: [d(TAGCGCTA) ]~.
Sophia ~ang , Marc Delsuc +, George Levy, Philip Borer and Stev~n
LaPlante , NMR and Data Processing Laboratory, NIH Resource and
Biophysics Program, Syracuse University, Syracuse, NY13244-1200.
+ICSN-CNRS 911 90, Gif-Sur-Yvette, France.
The solution structure of [d(TAGCGCTA)] has been solved by
NOESY-distance-restrained simulations. S~ructures determined by
different methods were systematically compared (e.g. restrained
dynamics and distance geometry analysis). Assignments have been
completed for all the non-exchangeable proton resonances using NOESY
and double quantum filtered COSY. NOESY spectra were acquired at 50,
i00, 200, 400, 800 and 1200 msec. Volumes were obtained by several
integration algorithms and those methods were compared. Completely
isolated peaks and well resolved crosspeaks were used in the
analysis. Distances were calculated from comparison of the initial
NOE build-up rate with the reference distances (i.e. H2'-H2", H5-H6).
I 91 OPTIMIZATION OF NMR DATAPROCESSING WITH PARALLEL
COMPUTERS: Roy E. Hoffman* and George C. Levy, Northeast Parallel
Architectures Center and NIH Resource, Bowne Hall, Syracuse
University, Syracuse, NY 13244-1200, USA.
For 40 years, most computers have been based on a single
processor in what is known as the Von Neumann architecture. In
the early 1970's, vector and array processors were introduced for
scientific data processing and subsequently for NMR data
reduction. It is only recently that computers with parallel
processors have become widely available to NMR researchers and
the advent of compilers with parallel and vector optimization
has enabled the modification of algorithms in order to achieve
speeds previously only possible with supercomputers.
In this work an Alliant FX/80 system was used. This contains
8 parallel processors, each with a vector facility, and has a
maximum performance speed of 189 Mflops. With a physical memory
of 128 Mbytes and a virtual memory of 2 Gbytes it is ideal for 2D
and 3D-NMR processing.
iD-Fourier transforms are 20 times faster on the Alliant
than on a VAX 8800 and 120 times faster than on a VAX 11/750.
However, the speed o~ a single processor on the Alliant when used
without vector optimization is comparable to a VAX 8800. We
report increases of computational speed for other algorithms such
as 2D lineshape analysis, plotting, and peak-picking. These
increases in speed are achieved in part by the optimization
facilities in the compiler but much of the enhancement arises
from changes in the source code.
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