%-------------------------------------------------------------------------------
% UF Sparse Matrix Collection, Tim Davis
% http://www.cise.ufl.edu/research/sparse/matrices/Williams/pdb1HYS
% name: Williams/pdb1HYS
% [Protein: protein data bank 1HYS.  Williams et al.]
% id: 2373
% date: 2008
% author: S. G. Sarafianos et al
% ed: S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel
% fields: name title A id date author ed kind notes
% kind: weighted undirected graph
%-------------------------------------------------------------------------------
% notes:
% 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.                                                           
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