Software Profiling & Testing

Two types of software profiling were performed: (1) back-end software testing, and (2) front-end testing of the web interface. Both types of profiling were performed on the server that currently houses the KINARI webpage. The back-end software testing was performed on more than 25,000 proteins retrieved from the Protein Data Bank (PDB), and was conducted to test each of the four curation steps and the rigidity analysis phases of KINARI. The profile testing of the front-end graphical user interface was performed to evaluate the visualizer and front-end features of KINARI-Web.

For the back-end profile testing, the following five components of KINARI were tested: (1) Curation - Cleaning a PDB file, (2) Curation - Adding Hydrogens, (3) Curation - Calculating Interactions, (4) Curation - Removing Unwanted Interactions, and (5) Performing Rigidity Analysis. Several separate PDB data sets were used, each with different sized proteins. Also, the curation and modeling options were varied across several of the profile runs to test how the different components of KINARI and KINARI-Web perform under various combinations of options that a user might designate. For each data set, the PDB IDs are made available, the log file, as well as a PNG and PDF plots of the average run time of each curation and rigidity analysis step vs. the number of residues.

For the front-end testing, each step of KINARI-Web was invoked, including downloading, cleaning/curating a PDB file, performing rigidity analysis, and generating output files necessary to render the protein and the results in the visualizer.

Below we provide information about the PDB files in each data set, profiling results, as well as plots of Average Execution time versus Number of Residues for each profiling run.


Profile Testing Summaries

Back-End Profile Testing, Composite Results
(click on plot to view full-size pdf version)
Front-End, Curation and Visualizer Profile Testing, Overview
# Proteins 63
Largest Protein 558 Residues
18,098 Atoms
Smallest Protein 104 Residues
1,669 Atoms
Curation, 104 residue protein 2.1 Seconds
Rigidity Analysis, 104 residue protein 2.0 Seconds
Curation + Rigidity Analysis, 104 residue protein 4.1 Seconds
Curation, 558 residue protein 183.2 Seconds
Rigidity Analysis, 558 residue protein 219.5 Seconds
Curation + Rigidity Analysis, 558 residue protein 402.7 Seconds


Back-end Software Profiling - Results By Dataset

Back-end Testing, Data Set 1 -- (click on plot to view full-size pdf version)
Number of PDB Files : 528
PDB IDs in Data set (.txt file)
Number of Chains (Asymmetrical units) : 1
Number Total Residues : 50-100 residues
Experimental Setup : X-Ray, removed at 95% similarity
Retain All Chains : Yes
Retain All Waters : No
Prune Interactions : No
Profiling Results (.txt file)
Run-Time VS Residue Length Plot (.pdf File)

Back-end Testing, Data Set 2 -- (click on plot to view full-size pdf version)
Number of PDB Files : 3,491
PDB IDs in Data set (.txt file)
Number of Chains (Asymmetrical units) : 1
Number Total Residues : 101-250 residues
Experimental Setup : X-Ray, removed at 90% similarity
Retain All Chains : Yes
Retain All Waters : No
Prune Interactions : No
Profiling Results (.txt file)
Run-Time VS Residue Length Plot (.pdf File)

Back-end Testing, Data Set 3 -- (click on plot to view full-size pdf version)
Number of PDB Files : 2,108
PDB IDs in Data set (.txt file)
Number of Chains (Asymmetrical units) : 1
Number Total Residues : 251-500 residues
Experimental Setup : X-Ray, removed at 90% similarity
Retain All Chains : Yes
Retain All Waters : No
Prune Interactions : No
Profiling Results (.txt file)
Run-Time VS Residue Length Plot (.pdf File)

Back-end Testing, Data Set 4 -- (click on plot to view full-size pdf version)
Number of PDB Files : 495
PDB IDs in Data set (.txt file)
Number of Chains (Asymmetrical units) : 1
Number Total Residues : 501-1000 residues
Experimental Setup : X-Ray, removed at 90% similarity
Retain All Chains : Yes
Retain All Waters : No
Prune Interactions : No
Profiling Results (.txt file)
Run-Time VS Residue Length Plot (.pdf File)

Back-end Testing, Data Set 5 -- (click on plot to view full-size pdf version)
Number of PDB Files : 3297
PDB IDs in Data set (.txt file)
Number of Chains (Asymmetrical units) : 2-5
Number Total Residues : 50-300 residues
Experimental Setup : X-Ray, removed at 90% similarity
Retain All Chains : Yes
Retain All Waters : No
Prune Interactions : No
Profiling Results (.txt file)
Run-Time VS Residue Length Plot (.pdf File)

Front-end Profile Testing - Detailed Results

The front-end of KINARI-Web was analyzed on 63 proteins. During each profile run , the download, curation, model building, rigidity analysis, and visualization features of KINARI-Web were invoked, and the execution times were recorded. Detailed Profiling results are provided for 13 proteins, and summary results are provided for the other 50.

PDB ID Number Of Residues Number Of Atoms Outcome Curation Download Time (seconds) Curation Execution Time (seconds) Curation Total Time (seconds) Curation Export Time (seconds) Rigidity Analysis Total Time (seconds) Total Curation + Rigidity Analysis Time Curation Log
1hrc 104 1669 Success 0.291 1.892 2.185 0.001 2.005 4.320 1hrc_Report.txt
1fto 263 7680 Success 0.265 31.368 31.713 0.004 37.971 70.078 1fto_Report.txt
1a2p 110 5,085 Success 0.335 13.954 14.363 0.0017 17.179 31.544 1a2p_Report.txt
1j4p 151 2,627 Success 0.216 4.171 4.452 0.001 4.161 8.696 1j4p_Report.txt
1hka 158 2,351 Success 0.189 3.758 3.999 0.001 4.510 8.512 1hka_Report.txt
1kkl 305 11,376 Success 0.346 68.906 69.337 0.004 76.410 148.120 1kkl_Report.txt
1cbu 180 8,202 Success 0.286 35.534 35.894 0.003 41.036 77.578 1cbu_Report.txt
1ex6 186 5,777 Success 0.326 18.262 18.639 0.003 20.451 39.090 1ex6_Report.txt
1dvr 220 6,782 Success 0.263 24.204 24.542 0.003 27.413 53.516 1dvr_Report.txt
1fin 558 18,098 Success 0.466 182.660 183.227 0.009 219.598 401.933 1fin_Report.txt
1lio 363 4,797 Success 0.218 13.275 13.567 0.002 15.292 28.859 1lio_Report.txt
1cmk 377 5,989 Success 0.345 19.814 20.201 0.002 22.748 42.950 1cmk_Report.txt
16pk 415 6,367 Success 0.351 21.727 22.128 0.004 26.303 48.432 16pk_Report.txt



Front-end Profile Testing - Curation, Summary

The below results detail the run-times for the curation portion of KINARI-Web for 50 randomly selected proteins.

PDB ID Success Download Time Curation Execuation Time (seconds) Curation Processing Time (seconds) Curation Total Time (seconds)
1A1A yes 0.007 7.148 0.077 7.245
1A1O yes 0.009 26.595 0.126 26.742
1A92 yes 0.006 7.580 0.092 7.688
1AFU yes 0.006 8.908 0.075 9.000
1AY7 yes 0.006 5.851 0.068 5.941
1B44 yes 0.012 44.986 0.181 45.191
1BMS yes 0.010 20.068 0.166 20.255
1BSC yes 0.013 16.486 0.093 16.602
1BZ9 no 0.004 1.542 1.557
1CT4 yes 0.006 8.216 0.061 8.294
1DSF yes 0.006 8.439 0.061 8.517
1ETY yes 0.005 4.107 0.068 4.191
1EZG yes 0.005 3.299 0.043 3.359
1F2K yes 0.006 9.481 0.059 9.558
1FIV yes 0.005 2.296 0.049 2.361
1G7M yes 0.006 19.85 0.090 19.95
1HXL yes 0.006 10.921 0.079 11.021
1HXZ yes 0.006 11.294 0.072 11.384
1I3Z yes 0.004 2.117 0.063 2.197
1IGC yes 0.011 36.428 0.120 36.570
1IGM yes 0.007 8.979 0.082 9.080
1M46 yes 0.005 4.550 0.072 4.638
1MBV yes 0.005 9.067 0.086 9.171
1MBY yes 0.007 4.439 0.060 4.524
1MFL yes 0.005 1.615 0.038 1.671
1MI0 yes 0.007 2.512 0.041 2.571
1NKN yes 0.007 15.608 0.118 15.745
1OVO yes 0.005 6.601 0.082 6.698
1P5U yes 0.009 33.161 0.129 33.310
1QOJ yes 0.004 1.505 0.050 1.572
1QQK yes 0.007 9.207 0.116 9.342
1QZ7 yes 0.011 43.155 0.176 43.352
1R1T yes 0.005 6.504 0.110 6.630
1R8O yes 0.005 4.243 0.066 4.326
1RFB yes 0.006 8.496 0.096 8.609
1RU0 yes 0.006 6.967 0.071 7.058
1S7Q yes 0.008 26.6185 0.115 26.753
1T2L yes 0.007 10.357 0.093 10.469
1U5Y yes 0.012 25.734 0.108 25.865
1U6L yes 0.005 8.858 0.106 8.981
1UFI yes 0.007 6.628 0.082 6.728
1VFA yes 0.006 8.560 0.072 8.648
1VFB yes 0.009 20.737 0.096 20.853
1WDF yes 0.005 5.175 0.087 5.277
1WWH yes 0.007 16.027 0.124 16.169
1XPS yes 0.007 9.116 0.086 9.220
1YCR yes 0.004 2.051 0.047 2.114
1YLM yes 0.007 13.578 0.094 13.691
1YWO yes 0.003 0.918 0.040 0.972