New folds

Aim: we want to test also the ability of the servers to recognise new fold, because this is the main issue and purpose of these servers. Although we don’t have any new folds, we can use the structures, which don’t have any structural similarity according to CATH.

I have chosen one structure from each of classes in CATH, which doesn’t have any structural similarity and run it with servers.

Server	1bgf (min)	1pmi (min)	1pya	1cii (min)
CE		210		92
Dali	6	3		3
Dejavu	22	7	74	91
Lock	6	8		5
Matras	7	11		6
Pride	sec	sec	sec	sec
SSM	1	1	2	1
Top	30	10		51
Tops	2			1
Topscan	Sec	Sec		Sec
Vast	5	10		7

I don’t have times for 1pya because of our x-ray main disc crash for all of the servers except of Dejavu too and SSM, which I run lately.

1. mainly α example – 1bgf (Stat-4) transcription factor, N domain – 124 aa, 1,45 Å, 77 % SSE

Dejavu – found 1bgf with Z-score = 31,85 and 124 aligned residues, second hit with Z-score = 13,28 and 60 aligned residues

Vast – found two hits – itself with P-value 10 e ^–7 and second hit (1e68:A) with P-value = 0,0286

Tops – 1bgf on the first rank, but two others with with score 2 and another more than 25 with score lower than 10.

Dali – 1bgf with Z-score = 25,8 and second rank with Z-score = 4,5

Lock – didn’t find even itself, because the structure is from 1998, first hit with 56 aligned residues and rmsd = 1,521

Matras – 1bgf on the first rank with Z-score = 44,18 and second match with Z-score = 6,80

Topscan – 1bgf on first rank with 100 % score, second 1pwb with score 75 %

CE – 220 hits, but second match has only 46 aligned residues and Z-score = 4,6

Top – 1bgf first, second hit has 56 aligned residues.

SSM – server found only the query 1bgf and nothing else…

Pride – didn’t find 1bgf at all, many hits (mostly helical proteins), first hit with score 0.738

2. mainlyβ example –1pmi (phosphomannose isomerase, domain 1 – length 185 aa)
1. 1,7 Å, 51 % SSE
   
   Dali – 1pmi with Z-score = 25,6 and second rank has only Z-score = 7,7
   
   Vast – 1pmi P-value = 10e^-27 and second rank has P-value = 0, 002
   
   Top – only four hits, 1 pmi has 16 aligned SSE, second hit has only 7
   
   Tops – 1pmi with score 4, sexond hit only with score 17
   
   Lock – didn’t find itself, first hit has 85 aligned residues and 1,775 rmsd
   
   Topscan - 1pmi with 100 % score and second hit with only 54,54 %
   
   Dejavu – no hits
   
   Matras – 1pmi with Z-score = 112,01 and second match with 18, 25
   
   CE – three different results, one of them contains 1pmi as a only one hit with 144 aligned residues and Z-score = 7,0 and other Z-score = 5,0, while providing also 16 neighbours, Z-score for second match is 3,9

SSM – didn’t find anything

Pride – didn’t find 1pmi at all, many hits (mostly mixed alpha-beta proteins), first hit with score 0.824

3. α-β example – colicin ia, domain 2 ; 1cii – 101 aa, 3,0 Å, 67 % SSE

Dali – 5 hits, 1cii with Z-score = 20, 6 and second 1fiq with Z-score = 4,0

Vast – found only itself

Dejavu - didn’t find itself, first hit with Z-score = 10,66 and 47 aligned residues

Tops – 5 hits with score =0 and 125 hits with score lower than 10

Matras – 25 hits, 1cii with Z-score = 36,37 and second with Z-score = 7,64

Lock – didn’t find itself, first result 1lvl has 44 aligned residues

Topscan – 1cii with 90 % score and second hit with 70 % score

Top – a lot of results; 1cii has 101 aligned residues and 5 SSE, while second hit 1pya has 45 aligned residues and 3 SSE.

CE - 1cii with Z-score = 6,3 and 101 aligned residues and second hit 1svf has score 3,9 and only 26 aligned residues

SSM – didn’t find anything at all

Pride – didn’t find 1cii at all, many hits (mostly mixed alpha-beta proteins), first hit with score 0.705

4. few secondary structure elements example – 1pya – pyruvoyl-dependent histidine decarboxylase (81 residues), 2,5 Å, 52 % SSE – (this is CATH classification)

Dali, Vast, CE – no hits except of 1pya

Top – 1pya has 81 aligned residues and second hit only 16

Matras – 1pya with Z-score = 64,99, second hit with Z-score = 7,76

Lock – 1pya has 81 aligned residues and second hit has 38 aligned residues

Topscan – six results with score 100 % and a lot of results with score 90 %

Tops –didn’t work (“No hydrogen bonds or chiralities were detected in target domain”)

Dejavu – did not find itself, first hit with Z-score = 8,11 and 30 aligned residues.

SSM – found only the query structure 1pya

Pride – found 1pya as the best hit, but with score 0.666, many other hits (mostly mixed alpha-beta proteins), second hit with score 0.509

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