arbitrary that can always yield a unique result for a given benchmark dataset, and hence has been increasingly used and widely recognized by investigators to examine the accuracy of various predictors [51–55]. In our case, we are not attempting prediction. Instead we are extracting statistically significant data from a large set of experimental observations. Protein Dataset In order to avoid homology bias and remove the redundant sequences from the benchmark dataset, a cutoff threshold of 25% should be used [49,56]. However, in this study we did not use such a stringent criterion because the currently available data do not allow us to do so. Otherwise, the numbers of proteins for some cases would be too few to have statistical significance. A list of high resolution protein chains (resolution #3.0 A˚) with sequence identity #35% was retrieved from the Pisces server [57]. All structures had a minimum chain length of 40 and a maximum R value – a measure of how well the experimental data can be predicted from the refined model - of 1.00. Non-X-ray structures and structures only with Ca atoms were excluded. The Pisces culling method selected was ‘‘chain’’. The downloaded list contained 9039 chains, present in 8598 different .ent files. The .ent files were downloaded from the Research Collaboratory for Structural Bioinformatics (RCSB) [58]. The corresponding .hssp files were downloaded from the homology-derived secondary structure of proteins (HSSP) database [59]. Entries in the Pisces list for which the corresponding .hssp files were not available were discarded, leaving 8272 .ent files with corresponding .hssp files. Amino Acid Pairs in Proteins These files contained 8706 of the non-redundant chains from the Pisces list. Software Three software packages were developed: ProExtract, ProPack and ProPair (Fig. 2). In addition specific programs were written to define the solvent shells as well as amino acid solvent accessibility distributions. All programs were developed using MATLAB v7 (2010a) [60]. The source code of the programs ProExtract (used to create the 8D tensor), ProPack (the query program that allows the user to access the 8 dimensional data tensor) and ProPair (the query program that allows the user to select a particular set of cells in the data tensor and which retrieves a list of proteins with specific pairs) have been uploaded as supplementary information. The file names are: ProExtract files. ‘‘ProExtract_V2p4.m’’, ‘‘ProExtract_V2p4.fig’’ to be found in Figure S1. ProPack files. ‘‘ProPack.m’’, ‘‘ProPack.fig’’ to be found in Figure S1. ProPair files. ‘‘PairFinder_v1p2.m’’, ‘‘PairFinder_v1p2.fig’’, ‘‘PairSearcher_v1p1.m’’ to be found in Figure S1. The description on how to run the software ProExtract, ProPack and Propair can be found in Figure S1: ‘‘ProExtract_ User instructions.doc’’, ‘‘Propack_User instructions.doc, ‘‘Pro- Pair_user instructions.doc’’, respectively. As mentioned in Figure 2, in order to run ProExtract, two input files are needed: the protein.ent list and the list of correspondent hssp files. A file named ‘‘pisces_35_id_files_with_hssp.txt’’ has Figure 2. Flowchart depicting the main programs built in order to carry out the presented data as well as the input and output files needed by each program. AA1 is amino type 1, AA2 amino type 2, SA is the solvent accessibility of the protein shell where the selected amino acid pair is located, Dist is the spatial distance between the selected amino acids, SS1 is the secondary structure of AA1, SS2 is the secondary structure of AA2, sequence distance is the primary sequence distance between the amino acid residues selected, chain length is the length of the chain being analyzed. doi:10.1371/journal.pone.0025638.g002 PLoS ONE | www.plosone.org 3 December 2011 | Volume 6 | Issue 12 | e25638