W530 Nucleic Acids Research, 2009, Vol. 37, Web Server issue matched motifs (the results are available at: http://proda ta.swmed.edu/ProSMoS/compattern/plait.htmlresult/ index.html). In SCOP, these PDBs are attributed to 46 folds and 100 superfamilies, showing that this is a Figure 2. Representative ferredoxin-like motif hits. b-Strands shown in yellow and a-helices shown in cyan. The ﬁrst residue of the motif is colored green and the ﬁrst residue of each SSE is colored purple. (A) The best-scoring motif hit, pdb id 1sc6, chain D, D-3-phosphoglycerate dehydrogenase, residue ranges 337–346, 347–362, 364–373, 375–384, 386–400, 402–410. (B) The weakest-scoring motif hit (#8299), pdb id 3b8m, chain B, bacterial polysaccharide co-polymerase, residue ranges 64–74, 99–114, 152–157, 171–179, 180–251, 320–324. (C) The hit #482, pdb id 2az1, chain E, nucleoside diphosphate kinase, residue ranges 6–13, 20–33, 34–43, 73–81, 83–93, 117–121. (D) The hit #4750. This motif overlaps with #482 (C) over 5 SSEs, 6–13, 20–33, 34–43, 73–81, 104–110, 117–121, with the second helix being distinct (residue range 104–110, colored red). Since this helix is shorter than in (C), this motif scores worse. (C) and (D) illustrate the possibility of overlapping motifs being found by the server. very common pattern in protein structures. It is interesting to see that about 50 diﬀerent SCOP folds have a ferre- doxin-like motif in their structures. Figure 2A shows the ﬁrst hit (pdbid 1sc6, SCOP domain d1sc6d3 ferredoxin- like SCOP fold). This is a very typical and structurally compact ferredoxin motif with ideal SSE lengths and good SSE packing. In contrast, Figure 2B shows the hit #8299 (pdbid 3b8m, not classiﬁed in SCOP, bacterial poly- saccharide co-polymerases which is located in the inner membrane and plays important role in the control of the chain length distribution of complex polysaccharides). In this motif, the second helix is very long (colored red in Figure 2B). Between the third strand and the last strand, there is a long a helical hairpin which comprises the long helix (the second helix in motif, red) extending about 100 A˚ into the periplasm and three additional helices folding back (20). This hit, although undoubtedly containing ferredoxin-like pattern, are not scored very high by ProSMoS due to the long helix. Similarly, Figure 2C (rank #482) and Figure 2D (rank #4750) show a pair of two overlapping motifs found in the same protein domain (pdb id 2az1, motifs located in the range of SCOP domain 2az1e1, ferredoxin-like fold). It is clear that #482 is a better match to ferredoxin-like fold than #4750, as the second helix is too short in the latter. The speed of complete PDB database search ProSMoS server completely enumerates all candidate motif hits for a user-deﬁned query, thus the search is time-demanding. Moreover, running time may vary among diﬀerent queries, as it largely depends on query complexity and abundance. To illustrate the speed of ProSMoS Server, we carried out the searches for eight wide-spread structure patterns against the target database built on complete PDB (the largest database to use), and recorded the response time for each job. The response times are shown in Figure 3 with the average response time being about 20 min, which we ﬁnd acceptable for this time-demanding task. The results for the eight Figure 3. Response time of ProSMoS Server for eight wide-spread structure patterns in complete PDB database. The response time (min) is recorded from the submission of a job to the receipt of result for each structure pattern.