Description: Protein: protein data bank 1HYS. Williams et al.
|(undirected graph drawing)|
|number of rows||36,417|
|number of columns||36,417|
|# strongly connected comp.||1|
|explicit zero entries||0|
|nonzero pattern symmetry||symmetric|
|numeric value symmetry||symmetric|
|author||S. G. Sarafianos et al|
|editor||S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel|
|kind||weighted undirected graph|
Matrices used by S. Williams et al for sparse matrix multiplication on GPUs. 14 matrices were used in the following paper: S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, "Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms", Parallel Computing Volume 35, Issue 3, March 2009, Pages 178-194. Special issue on Revolutionary Technologies for Acceleration of Emerging Petascale Applications. https://hpcrd.lbl.gov/~swwilliams/research/papers/parco08_spmv.pdf http://dx.doi.org/10.1016/j.parco.2008.12.006 This same set of 14 matrices was also used in a subsequent technical report by NVIDIA: http://www.nvidia.com/object/nvidia_research_pub_001.html "Efficient Sparse Matrix-Vector Multiplication on CUDA" Nathan Bell and Michael Garland, in, "NVIDIA Technical Report NVR-2008-004", December 2008 file Name dim* nnz description dense2 Dense 2K 4.0M dense matrix in sparse format pdb1HYS Protein 36K 4.3M protein data bank 1HYS consph FEM/Spheres 83K 6.0M FEM concentric spheres cant FEM/Cantilever 62K 4.0M FEM cantilever pwtk Wind Tunnel 218K 11.6M pressurized wind tunnel rma10 FEM/Harbor 47K 2.37M 3D CFD of Charleston Harbor qcd5_4 QCD 49K 1.90M quark propagators (QCD/LGT) shipsec1 FEM/Ship 141K 3.98M FEM Ship section / detail mac_econ_fwd500 Economics 207K 1.27M Macroeconomic model mc2depi Epidemiology 526K 2.1M 2D Markov model of epidemic cop20k_A FEM/Accelerator 121K 2.62M Accelerator cavity design scircuit Circuit 171K 959K Motorola circuit simulation webbase-1M webbase 1M 3.1M Web connectivity matrix rail4284 LP 4Kx1.1M 11.3M Railways set cover, constraint matrix (*) the matrix is square if only one dimension listed. Six of the matrices are nearly identical to the matrices already in the UF Collection. They are thus not included in the UF Collection. See the README.txt file for this collection for details. I presume the pdb1HYS matrix comes from this source: http://www.rcsb.org/pdb/explore.do?structureId=1HYS http://dx.doi.org/10.2210/pdb1hys/pdb Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. Sarafianos, S.G., Das, K., Tantillo, C., Clark Jr., A.D., Ding, J., Whitcomb, J.M., Boyer, P.L., Hughes, S.H., Arnold, E. Journal: (2001) EMBO J. 20: 1449-1461 PubMed: 11250910 PubMedCentral: PMC145536 DOI: 10.1093/emboj/20.6.1449 Search Related Articles in PubMed PubMed Abstract: We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease... [ Read More & Search PubMed Abstracts ] We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The "RNase H primer grip", consisting of amino acids that interact with the DNA primer strand, may contribute to RNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent. An unusual "unzipping" of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage.
|null space dimension||6|
|full numerical rank?||no|
|singular value gap||137371|
|singular values (MAT file):||click here|
|SVD method used:||s = svd (full (A))|
For a description of the statistics displayed above, click here.
Maintained by Tim Davis, last updated 12-Mar-2014.
Matrix pictures by cspy, a MATLAB function in the CSparse package.
Matrix graphs by Yifan Hu, AT&T Labs Visualization Group.