Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

Algorithm 1

A pseudo-code of the MCPSC computation implemented in this work. The USM jobs are processed sequentially, while CE and TMalign pairwise structure comparison jobs are executed in parallel. Task par_calc_psc_dist assigns each PSC job to a free PE (node in a many-core and thread in multicore). If n is specified, the job’s assignment is fixed; otherwise the next free PE available is employed.

Data:

: query protein structures,

: database of known protein structures

// Sequential processing

calc_usm_dist(, )

// Parallel processing

for    in [CE, TMalign]  do

   for   in   do

     for   in   do

      jobs.add(in PE , using method , protein pair )

     end

   end

end

Par_calc_psc_dist(jobs)