T0468

Targets
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T0468

putative lipoprotein from Bacillus cereus

Target type: Human/Server

Target sequence:

>T0468 BcR103A, Bacillus cereus, 109 residues
MERASLNRIGKDVYYMQIKGEGTIEKVDGRNLRNYTLPAYDEDGVKKQITFRSTKKENDHKLNKYAFLRLYVDQDDNSKNEISSIEVKSYEEIQKADLPEKVKDKFTIK

Structure:
Method: NMR
Determined by: NESG
PDB ID: 2k5w

PyMOL of 2k5w

Domains:  PyMOL of domains

Single domain protein with poorly structured termini (mostly N-) and loops. Structurally variable regions were removed from NMR models for evaluation of predictions.

Structure classification:

OB-fold. 5-stranded β-barrel, which in contrast to most OB-fold members is open between the 3rd and the 5th β-strands. The five strands are shown in the ribbon diagram below as dark blue, cyan, green, yellow and orange. In addition to the 5-stranded OB-core, this structure is elaborated with a long insertion between β-strands 1 and 2 housing a β-hairpin (which is an extension of the hairpin 1-2), and two C-terminal α-helices.

CASP category:

Fold recognition. Fold similarity not detectable statistically by sequence methods known to us.

Closest templates:

The first COMPASS hit to OB-fold proteins is to the Nucleic acid - binding domain superfamily:

Subject = d1gm5a2   b.40.4.9  RecG "wedge" domain
length=180 filtered_length=178 Neff=17.669 Smith-Waterman score = 41 Evalue = 4.14e+01
QUERY         5      SLNRIGKDVYYMQIKGEGTIEKVDGRNLRNYTLPAYDEDGVKKQITFRSTKKENDHKLNKYAFLRLY==VDQDDNskneISSIEVKSYEEIQKADLPEKVKDKF  106
CONSENSUS_1   5      QLNPIGGDEYYVQITGDGKKKGEKGDGGYSYTLKGYDEDGKEKEVTFTAGKKELDHNLRKGAYLKLY==VKGKKG....IKGIEVTSWEEVKKEDIPKKALEKL  106
                     +++ ++ +E ++ +    ++++ ++ +G  +++   D++G+ + V F+ + ++L + L++GA L ++  V+ ++G    ++++++ ++E ++ E+  ++ L+ +
CONSENSUS_2   53     PIAELRPGEKVTVAGIVVSVRVIRTKRGKMLIVTLEDGTGSLELVFFNGVYAKLKKLLKVGARLLVSGKVERFDG~~~~GLQLVHPDYELLDEEEALEGRLVPV  152
d1gm5a2       53     KLNDLLPGEKVTTQGKIVSVETKKFQNMNILTAVLSDGLVHVPLKWFNQDYLQTYLKQLTGKEVFVTGTVKSNAY~~~~TGQYEIHNAEVTPKEGEYVRRILPI  152

However, this is the hit #41 in the total list of hits and its E-value is around 41 (which indicates BTW how good COMPASS E-value estimate is), so it can hardy be called statistically significant. Moreover, proteins from all SCOP classes were found by COMPASS prior to this hit. Nevertheless, 9 consensus match residues from the above alignment were selected among 16 and shown as "dots" on the two OB-fold structures, map to structurally equivalent positions validating the COMPASS alignment:

According to structure, proteins from 'Nucleic acid - binding' superfamily are also most similar to T0468, and those include phage ssDNA - binding proteins with an open barrel.

Target sequence - PDB file inconsistencies:

NMR models contain two C-terminal residues 110-LE-111, not present in the target sequence. This regions was removed from NMR models due to disorder anyway.

T0468    2k5w.pdb    T0468.pdb    PyMOL    PyMOL of domains   

Residue change log: remove 110-LE-111 as it is not present in target sequence; remove 1-MERASLNRIG-10, 56-KEND-59, 77-NSKNEISS-84 by 3.5Å SD cutoff;

Single domain protein: target 11-55, 60-76, 85-109 ; pdb 11-55, 60-76, 85-109

Sequence classification:

DUF1093 in Pfam, which includes just a few very close homologs. Below is PROMALS3D alignment of several most distant homologs detectable by PSI-BLAST. This alignment was not edited manually and may have errors. Biological sequences contain signal peptide (predicted as a helix at the N-terminus) not included in the target sequence.

Conservation:    9   7                                               9      5                 7    6      5      5               555                 9     6     5                                              
T0468         1  M--ERA----------------------------------SLNR--IGKDVYYMQIKGEGTIEKVDG-----RNLRNYTLPAYDED---GVKKQITFRSTKKENDHKLNKYAFLRLYVDQDDNSKNEISSIEVKSYEEIQKADLPEKVKDKFTIK------------------------------------  109
T0467         1  M---------------------------------------DLNR--MGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKD---GKEKELEFTAQ-----KNLRKEAFLRVYHSDK---------KGVSAWEEVKKDELPAKVKEKLGVK------------------------------------   97
gi_163762713  1  M--KKT--------IIILISTLVSLAVIAVVII---ATI-DFNR--VGKDHAYTLITENGDTEETVTGSGEVFTRYHYSQSAFTDE---GEEITVSFSSH-----KNLRHGAYLRLYMNH----------TDVTSYDEVQTEDVPAQALETLMQE------------------------------------  121
gi_116334877  1  ----KG-----------------------------IGTIDRFDPF-LSYKVGYTKLPSEKEISPNNK------ATNGYWTAWFTDNTMGNEWTKLTLTTGL----NPGVKNPYVMAYHKG----------SYVKVARIVPRTYINQTYVSNLAALDALLNHKGNTATNNHDLKKYKTQIHISDTVQQLVTE  137
gi_49398117   1  M--KRT--------LIIV--TIVLLIIILSLLLVRNEHLDRFNPL-LKEKVSYAKVPKDT--------------QDYRNITVYSKN---GEKKSYKLDFLG-----YDPTKEYVKVNHKG----------KYVRSIEYIT-KIFLAF--------------------------------------------  101
gi_116492027  1  M--RKG--------MIIS--GVVVVILLITF----GSAYFWYNSN-YGTQDYYTQIVDKGTKFVEKDDSNRSYVNYAYHQPAYNQA---SQKITVKFNGNL---ERPLKLHAYLKIGYNAKR--------NQVISWSKVDKKDVPKAALKQINP-------------------------------------  123
gi_69249191   1  M--KK---------LIGV--LVVL---GIFL----GGSFAAYHYF-YGGEAYYTKITTNGEMSATQADNGEKFTTYTYKQAAYNKD---GEKKQVTLREER---EHPLKMNAYLKLKVNPR---------KGVLSWEEIKASEVPKNAAEKIDN-------------------------------------  118
gi_116873589  1  MITKKR-------VLISL-----ATVLLAVCA-----IWEYAMPTDAAVKSYYLKVAEAGKPVKKN-----QFKGYEYTSKVYDDK---GKQKEIKFYSEK-----ELTKNEQFKVMIGEN---------KMVVNYKKIK--NVPDKIKYLAEK-------------------------------------  113
gi_65320434   1  M--NKRRNDYEDFVLCIL--GIGLPIYLLPFIL--RGDFDRFNPI-AEEKNVYAIAKGYGVPDYH------HKGRAMYSLKSFDES---GSRNEYTVGTST---PNDFIRKTYLRIHVKG----------KYVYSYEAISEKDIPEKIRKQLEV------EIK----------------------------  128
Consensus_aa:    M..c+.................................h..hp...h..cs.Yhbl...sp...pp......b....Yp..s@scp...tpp.phph........p....p.@l+l.hp...........p.V.shcblppp.ls..h.pph.......................................
Consensus_ss:                     h  hh hhhhhhhh                  eeeeeee     ee          eeeeeeeeee        eeeeeee              eeeeeee            eeeehhh  hhh  hhhhhhh                                       

Comments:

This protein is a close homolog of T0467:

PSIPRED  ------------EEEEEE----EEE-----------EEEEEEEEE-----EEEEEEE--------------EEEEEEE------------EEEEHHH--HHH--HHHHHHH---
T0468    MERASLNRIGKDVYYMQIKGEGTIEKV-----DGRNLRNYTLPAYDEDGVKKQITFRSTKKENDHKLNKYAFLRLYVDQDDNSKNEISSIEVKSYEEIQKADLPEKVKDKFTIK
T0467    MD---LNRMGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKDGKEKELEFTAQK-----NLRKEAFLRVYHSDK---------KGVSAWEEVKKDELPAKVKEKLGVK
PSIPRED  ------------EEEEEEE---EEEE-------EEEEEEEEEEEE-----EEEEEEE--------------EEEEEE--------------EEEEEEE------HHHHHHH---

This OB-fold was predicted de-novo by ROSETTA, which correctly indicated an open barrel. This prediction was very suggestive of the correct structure, because ROSETTA is biased towards local β-strand pairing, and OB-fold has a crossing loop to form H-bonds between β-strands 1 and 4, not to mention barrel closure present in most OB-folds with H-bonds between β-strands 3 and 5. Metaserver bioinfo.pl fails to find similarity to other OB-fold proteins. Although some servers used OB-folds as templates, it is unclear how significant those predictions are, as the templates were closed barrels and many severs used SH3-fold templates as well. The bias towards SH3 fold is likely caused by the C-terminal region, which shows strong local conformational similarity to Sso7d Chromo-domain DNA-binding proteins.

This similarity covers about 30 residues (half of Sso7d SH3-fold) and spans through a β-hairpin and two α-helices. The first helix is a single-turn helix characteristic of SH3 fold. Such a helix frequently structured as a 310-helix is present at this spatial location in the majority of SH3 fold proteins. Mutual orientations of the four secondary structural elements between the two fragments (from OB and SH3) is very similar, and sequence similarity reflects this.

2k5w   67 FLRLYVDQD[10]EVKSYEEIQKADLPEKVKDKFTI 107
2bf4_A 30 ISFTYDEGG----GKTGRGAVSEKDAPKELLQMLEK 61 
          EEEEEEEE     EEEEEEEEHHHH HHHHHHHHHH    

Therefore it is not surprising that servers find this similarity, in particular for T0467, which is a close homolog of T0468. However, upon closer inspection there are several positions with charged residues (highlighted red in the above alignment) aligned to hydrophobs (yellow). These positions have different exposure to solvent in the two structures and hint that the local similarity may not translate to global fold similarity. Indeed, the two C-terminal helices are essential core elements is SH3 structure of Sso7d, but are peripheral surface helices not contributing to the core in OB-fold of T0468. In addition, the surface of the hairpin buried in SH3 fold is exposed in T0468. These inconsistencies in hydrophobic patterns are very suggestive of global structural differences:

DALI-LITE does not detect similarity bewteen T0468 and Sso7d, but superimposes Sso7d with T0467, which is a close homolog of T0468. The central 3-stranded meander β-sheet in two proteins (shown in the back on the images above: blue-cyan-green on T0468 structure, while T0467 was superimposed, and green-yellow in Sso7d) is aligned, albeit with a very low Z-score of 0.3 (33 residues, RMSD 2Å). We agree that this is a globally meaningful alignment (only residues in capital letters are aligned), as it superimposes hydrophobic cores of both proteins.

DSSP   ....lllllllleeeeeELLLllLEEHhhhllllllLEEEEEEEEEllllLEEEEEEEELL..LLLLlleeeeeelllllllleeeelllllllhhhhhllllllllllll
2k5q   ....mdlnrmgkdeyyvQITVdgKEVHskadngqkyKDYEYKLTGFdkdgKEKELEFTAQK..NLRKeaflrvyhsdkkgvsaweevkkdelpakvkeklgvklehhhhhh
2bf4_A atvkfkykgeekevdisKIKK.vWRVG.........KMISFTYDEG....GGKTGRGAVSEkdAPKE..................................llqmlekqkk
DSSP   leeeeeelleeeeeehhHEEE.eEEEL.........LEEEEEEELH....HHLEEEEEEELllLLHH..................................hhhhhhhlll

As a summary, superposition of locally similar fragments does not result in a global superpositions of structural cores of the two folds, and does not result in a reasonable fold prediction. Vice versa, global superposition of the cores leaves the two locally similar fragments as non-equivalent parts of the two proteins, as they occupy very different spatial locations and carry out different structural roles.

Global similarity between OB and SH3 folds has been noticed previously1), and explained in terms of very distant evolutionary relationship (homology). It is possible that the two folds shared a common ancestor and are indeed homologous over the 3-stranded curved meander sheet, although definitive evidence for this is lacking. The meaning of the local fragment similarity between T0468 and Sso7d-like chromo-domain OB-fold proteins is unclear. It is conceivable that these similar fragments originated independently and conformational resemblance between them is due to chance.

Server predictions:

T0468:pdb 11-109:seq 11-109:FR;   alignment

click on a score in the table below to display the model in PyMOL

# GROUP ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ ↓ GROUP #
T0468 T0468 T0468 T0468
First score First Z-score Best score Best Z-score
1 Pcons_dot_net 52.01 42.62 55.55 2.03 2.06 1.60 52.01 42.62 55.55 1.67 1.66 1.28 Pcons_dot_net 1
2 Pcons_multi 51.44 39.56 59.97 1.97 1.67 2.03 51.44 43.30 59.97 1.61 1.75 1.72 Pcons_multi 2
3 Chicken_George 51.15 42.91 56.52 1.94 2.10 1.69 52.59 46.26 56.56 1.73 2.13 1.38 Chicken_George 3
4 FAMS−multi 50.00 41.00 56.40 1.83 1.85 1.68 50.58 41.95 58.74 1.53 1.57 1.60 FAMS−multi 4
5 Jiang_Zhu 50.00 38.31 47.96 1.83 1.51 0.85 50.00 38.31 48.48 1.47 1.10 0.57 Jiang_Zhu 5
6 SAMUDRALA 49.71 44.16 56.53 1.80 2.26 1.69 50.00 44.16 57.10 1.47 1.86 1.43 SAMUDRALA 6
7 3D−JIGSAW_V3 49.14 38.79 54.11 1.74 1.57 1.46 50.29 42.15 56.84 1.50 1.60 1.41 3D−JIGSAW_V3 7
8 Sternberg 49.14 38.79 54.11 1.74 1.57 1.46 49.14 40.90 54.11 1.38 1.43 1.13 Sternberg 8
9 3D−JIGSAW_AEP 48.85 41.95 56.81 1.72 1.97 1.72 50.29 43.49 56.81 1.50 1.77 1.40 3D−JIGSAW_AEP 9
10 RAPTOR 48.56 40.90 50.11 1.69 1.84 1.06 48.56 40.90 50.11 1.32 1.43 0.73 RAPTOR 10
11 MUSTER 48.56 37.64 51.31 1.69 1.43 1.18 48.56 37.64 51.31 1.32 1.01 0.85 MUSTER 11
12 3DShot1 48.56 34.58 52.35 1.69 1.04 1.28 48.56 34.58 52.35 1.32 0.61 0.95 3DShot1 12
13 KudlatyPredHuman 48.28 38.51 57.88 1.66 1.54 1.83 48.28 39.46 57.88 1.29 1.25 1.51 KudlatyPredHuman 13
14 Hao_Kihara 48.28 33.52 54.61 1.66 0.90 1.51 48.28 33.52 54.61 1.29 0.47 1.18 Hao_Kihara 14
15 mufold 47.99 39.27 55.89 1.63 1.63 1.63 47.99 39.27 55.89 1.27 1.22 1.31 mufold 15
16 PRI−Yang−KiharA 47.41 35.73 47.61 1.57 1.18 0.82 47.41 35.73 47.61 1.21 0.76 0.48 PRI−Yang−KiharA 16
17 LevittGroup 47.13 40.61 55.56 1.55 1.80 1.60 47.13 40.61 55.56 1.18 1.40 1.28 LevittGroup 17
18 Zhang 47.13 32.66 56.65 1.55 0.79 1.71 47.99 38.70 57.64 1.27 1.15 1.49 Zhang 18
19 fams−ace2 46.55 38.12 55.75 1.49 1.49 1.62 52.01 40.13 59.89 1.67 1.33 1.71 fams−ace2 19
20 Zhang−Server 46.55 36.97 54.93 1.49 1.34 1.54 46.55 36.97 54.93 1.12 0.92 1.21 Zhang−Server 20
21 McGuffin 46.55 36.97 54.93 1.49 1.34 1.54 48.56 37.64 54.93 1.32 1.01 1.21 McGuffin 21
22 FAMSD 46.55 35.82 47.64 1.49 1.19 0.82 46.55 35.82 48.90 1.12 0.77 0.61 FAMSD 22
23 Jones−UCL 46.26 38.98 52.50 1.46 1.60 1.30 46.26 38.98 52.50 1.09 1.18 0.97 Jones−UCL 23
24 circle 46.26 37.84 46.42 1.46 1.45 0.70 46.26 37.84 48.90 1.09 1.04 0.61 circle 24
25 SAINT1 44.83 39.46 50.62 1.32 1.66 1.11 44.83 39.46 50.62 0.95 1.25 0.78 SAINT1 25
26 MULTICOM 42.53 37.93 53.45 1.09 1.46 1.39 43.39 37.93 53.81 0.80 1.05 1.10 MULTICOM 26
27 TASSER 42.53 35.06 52.96 1.09 1.10 1.34 42.53 35.06 57.24 0.72 0.67 1.45 TASSER 27
28 Zico 40.80 36.40 50.10 0.92 1.27 1.06 46.84 37.26 55.27 1.15 0.96 1.25 Zico 28
29 ZicoFullSTP 40.80 36.40 50.10 0.92 1.27 1.06 47.99 37.84 55.19 1.27 1.04 1.24 ZicoFullSTP 29
30 3DShotMQ 40.80 32.18 43.74 0.92 0.73 0.44 40.80 32.18 43.74 0.54 0.30 0.09 3DShotMQ 30
31 pro−sp3−TASSER 40.23 36.21 48.90 0.87 1.24 0.95 48.28 39.46 56.91 1.29 1.25 1.41 pro−sp3−TASSER 31
32 A−TASSER 39.66 36.21 49.13 0.81 1.24 0.97 47.70 40.52 57.24 1.24 1.39 1.45 A−TASSER 32
33 BioSerf 38.22 31.13 43.28 0.67 0.60 0.40 38.22 31.13 46.91 0.28 0.16 0.41 BioSerf 33
34 RBO−Proteus 35.92 32.09 46.18 0.44 0.72 0.68 35.92 32.09 46.18 0.05 0.29 0.33 RBO−Proteus 34
35 huber−torda−server 35.92 28.83 32.93 0.44 0.30 -0.62 35.92 28.83 33.74 0.05 -0.14 -0.92 huber−torda−server 35
36 GS−KudlatyPred 35.34 31.03 43.67 0.39 0.58 0.43 41.09 35.73 43.67 0.57 0.76 0.08 GS−KudlatyPred 36
37 keasar 35.34 29.60 49.00 0.39 0.40 0.96 35.34 31.80 49.54 -0.01 0.25 0.67 keasar 37
38 POEM 35.06 31.03 41.71 0.36 0.58 0.24 35.34 31.03 50.83 -0.01 0.15 0.80 POEM 38
39 BAKER−ROBETTA 34.20 30.56 50.04 0.27 0.52 1.06 34.20 30.56 50.04 -0.12 0.09 0.72 BAKER−ROBETTA 39
40 TJ_Jiang 31.03 24.14 37.93 -0.04 -0.30 -0.13 31.03 27.49 38.54 -0.44 -0.31 -0.43 TJ_Jiang 40
41 FALCON 30.75 27.87 39.91 -0.07 0.18 0.07 31.32 28.07 40.45 -0.41 -0.24 -0.24 FALCON 41
42 POEMQA 30.17 25.57 40.62 -0.12 -0.11 0.13 34.77 31.13 50.83 -0.06 0.16 0.80 POEMQA 42
43 LEE 30.17 23.47 38.93 -0.12 -0.38 -0.03 30.17 25.57 47.05 -0.52 -0.56 0.42 LEE 43
44 ABIpro 29.89 25.96 42.16 -0.15 -0.06 0.29 29.89 26.15 42.93 -0.55 -0.49 0.01 ABIpro 44
45 POISE 29.60 27.59 43.42 -0.18 0.14 0.41 29.60 27.59 45.10 -0.58 -0.30 0.23 POISE 45
46 MUFOLD−MD 29.60 27.49 43.15 -0.18 0.13 0.38 35.63 30.65 43.15 0.02 0.10 0.03 MUFOLD−MD 46
47 SAM−T08−server 29.60 25.19 37.97 -0.18 -0.16 -0.13 29.60 25.19 38.80 -0.58 -0.61 -0.41 SAM−T08−server 47
48 MULTICOM−REFINE 29.31 26.82 40.22 -0.21 0.05 0.10 32.47 28.83 43.24 -0.29 -0.14 0.04 MULTICOM−REFINE 48
49 Sasaki−Cetin−Sasai 29.31 26.25 44.53 -0.21 -0.03 0.52 31.03 26.25 44.78 -0.44 -0.48 0.19 Sasaki−Cetin−Sasai 49
50 Elofsson 29.02 25.77 39.96 -0.24 -0.09 0.07 29.89 26.82 40.29 -0.55 -0.40 -0.26 Elofsson 50
51 MUProt 29.02 25.57 40.31 -0.24 -0.11 0.10 32.47 28.26 43.29 -0.29 -0.21 0.04 MUProt 51
52 MULTICOM−CLUSTER 29.02 25.38 40.00 -0.24 -0.14 0.07 37.93 33.14 43.58 0.26 0.42 0.07 MULTICOM−CLUSTER 52
53 GeneSilico 29.02 22.61 40.94 -0.24 -0.49 0.17 30.46 24.52 40.94 -0.50 -0.70 -0.19 GeneSilico 53
54 Handl−Lovell 28.45 25.77 34.42 -0.29 -0.09 -0.47 35.63 32.76 40.44 0.02 0.37 -0.24 Handl−Lovell 54
55 Bates_BMM 28.45 24.33 37.47 -0.29 -0.27 -0.17 47.13 40.42 49.86 1.18 1.37 0.70 Bates_BMM 55
56 SMEG−CCP 28.45 23.37 39.51 -0.29 -0.39 0.03 28.45 23.37 39.51 -0.70 -0.85 -0.34 SMEG−CCP 56
57 SAM−T08−human 28.16 23.28 40.30 -0.32 -0.40 0.10 34.48 28.35 48.63 -0.09 -0.20 0.58 SAM−T08−human 57
58 FLOUDAS 28.16 23.18 31.89 -0.32 -0.42 -0.72 43.10 35.06 46.85 0.77 0.67 0.40 FLOUDAS 58
59 LOOPP_Server 27.87 25.57 30.64 -0.35 -0.11 -0.84 44.25 37.74 46.91 0.89 1.02 0.41 LOOPP_Server 59
60 HHpred5 27.87 22.51 37.91 -0.35 -0.50 -0.13 27.87 22.51 37.91 -0.76 -0.96 -0.50 HHpred5 60
61 Ozkan−Shell 27.59 24.52 38.13 -0.38 -0.25 -0.11 28.74 26.63 38.27 -0.67 -0.43 -0.46 Ozkan−Shell 61
62 DBAKER 27.59 23.56 28.20 -0.38 -0.37 -1.08 59.48 53.54 70.89 2.42 3.08 2.82 DBAKER 62
63 Bilab−UT 27.59 22.80 39.71 -0.38 -0.47 0.05 28.74 26.63 41.26 -0.67 -0.43 -0.16 Bilab−UT 63
64 METATASSER 27.01 22.03 48.06 -0.43 -0.56 0.86 47.99 41.48 55.02 1.27 1.51 1.22 METATASSER 64
65 ZicoFullSTPFullData 26.72 22.61 47.73 -0.46 -0.49 0.83 47.99 37.84 55.19 1.27 1.04 1.24 ZicoFullSTPFullData 65
66 MULTICOM−CMFR 26.44 23.18 34.90 -0.49 -0.42 -0.43 26.44 23.18 34.90 -0.90 -0.88 -0.80 MULTICOM−CMFR 66
67 mariner1 26.44 22.22 32.93 -0.49 -0.54 -0.62 28.74 25.48 36.54 -0.67 -0.58 -0.63 mariner1 67
68 FEIG 26.44 20.69 35.66 -0.49 -0.73 -0.35 32.18 24.14 42.56 -0.32 -0.75 -0.03 FEIG 68
69 FFASsuboptimal 26.44 19.83 26.90 -0.49 -0.84 -1.21 26.44 21.07 30.65 -0.90 -1.15 -1.23 FFASsuboptimal 69
70 Phragment 26.15 22.41 39.67 -0.52 -0.52 0.04 26.15 23.66 40.19 -0.93 -0.81 -0.27 Phragment 70
71 Distill 25.86 22.61 39.20 -0.55 -0.49 -0.00 25.86 22.61 39.20 -0.96 -0.95 -0.37 Distill 71
72 PS2−server 25.57 23.47 33.20 -0.58 -0.38 -0.59 39.66 35.44 41.48 0.43 0.72 -0.14 PS2−server 72
73 Scheraga 25.57 22.41 33.67 -0.58 -0.52 -0.55 27.30 22.41 33.67 -0.81 -0.98 -0.92 Scheraga 73
74 MULTICOM−RANK 25.57 21.84 31.48 -0.58 -0.59 -0.76 27.30 22.22 38.84 -0.81 -1.00 -0.40 MULTICOM−RANK 74
75 SHORTLE 25.29 22.32 33.25 -0.60 -0.53 -0.59 25.29 24.14 34.68 -1.01 -0.75 -0.82 SHORTLE 75
76 Kolinski 25.29 21.46 35.53 -0.60 -0.64 -0.36 34.20 26.15 41.65 -0.12 -0.49 -0.12 Kolinski 76
77 ProteinShop 25.00 23.47 33.34 -0.63 -0.38 -0.58 25.57 23.47 37.45 -0.99 -0.84 -0.54 ProteinShop 77
78 fleil 25.00 22.32 27.79 -0.63 -0.53 -1.12 25.29 22.41 28.14 -1.01 -0.98 -1.48 fleil 78
79 MidwayFolding 24.71 21.36 32.26 -0.66 -0.65 -0.68 48.56 40.90 50.11 1.32 1.43 0.73 MidwayFolding 79
80 HHpred4 24.71 20.69 34.12 -0.66 -0.73 -0.50 24.71 20.69 34.12 -1.07 -1.20 -0.88 HHpred4 80
81 FFASflextemplate 24.71 20.11 22.91 -0.66 -0.81 -1.60 24.71 20.11 22.91 -1.07 -1.28 -2.00 FFASflextemplate 81
82 Phyre_de_novo 24.43 22.51 38.25 -0.69 -0.50 -0.10 30.75 25.10 39.76 -0.47 -0.63 -0.31 Phyre_de_novo 82
83 keasar−server 24.43 20.21 32.12 -0.69 -0.80 -0.70 24.43 21.46 32.12 -1.10 -1.10 -1.08 keasar−server 83
84 FFASstandard 24.43 18.10 22.49 -0.69 -1.07 -1.64 24.71 20.11 22.91 -1.07 -1.28 -2.00 FFASstandard 84
85 Phyre2 24.14 21.93 32.89 -0.72 -0.58 -0.62 33.05 27.30 41.92 -0.24 -0.34 -0.09 Phyre2 85
86 mGenTHREADER 24.14 21.07 19.08 -0.72 -0.69 -1.98 24.14 21.07 19.08 -1.13 -1.15 -2.39 mGenTHREADER 86
87 Wolynes 23.56 20.79 36.97 -0.77 -0.72 -0.22 24.71 22.80 40.02 -1.07 -0.93 -0.28 Wolynes 87
88 nFOLD3 23.56 20.11 30.41 -0.77 -0.81 -0.87 25.57 23.28 32.01 -0.99 -0.86 -1.09 nFOLD3 88
89 EB_AMU_Physics 22.99 20.88 33.97 -0.83 -0.71 -0.52 22.99 20.88 33.97 -1.25 -1.18 -0.89 EB_AMU_Physics 89
90 Softberry 22.70 21.55 30.46 -0.86 -0.63 -0.86 22.70 21.55 30.46 -1.27 -1.09 -1.25 Softberry 90
91 taylor 22.70 21.46 29.20 -0.86 -0.64 -0.98 26.15 21.46 31.98 -0.93 -1.10 -1.09 taylor 91
92 COMA 22.70 19.25 28.25 -0.86 -0.92 -1.08 22.70 20.40 30.70 -1.27 -1.24 -1.22 COMA 92
93 ACOMPMOD 22.70 17.34 21.96 -0.86 -1.16 -1.69 23.56 21.65 32.97 -1.19 -1.08 -0.99 ACOMPMOD 93
94 HHpred2 22.41 20.88 32.24 -0.89 -0.71 -0.69 22.41 20.88 32.24 -1.30 -1.18 -1.07 HHpred2 94
95 COMA−M 22.41 20.31 20.28 -0.89 -0.78 -1.86 22.70 20.31 29.18 -1.27 -1.25 -1.37 COMA−M 95
96 3Dpro 22.41 18.58 28.33 -0.89 -1.00 -1.07 25.57 22.32 31.96 -0.99 -0.99 -1.10 3Dpro 96
97 MeilerLabRene 22.13 19.83 30.50 -0.91 -0.84 -0.86 24.43 21.55 32.59 -1.10 -1.09 -1.03 MeilerLabRene 97
98 DistillSN 21.55 17.53 31.34 -0.97 -1.14 -0.77 23.56 20.69 31.34 -1.19 -1.20 -1.16 DistillSN 98
99 FALCON_CONSENSUS 20.98 20.02 31.27 -1.03 -0.82 -0.78 31.32 28.07 40.45 -0.41 -0.24 -0.24 FALCON_CONSENSUS 99
100 fais−server 20.98 19.35 36.81 -1.03 -0.91 -0.24 34.20 29.98 40.86 -0.12 0.01 -0.20 fais−server 100
101 StruPPi 20.98 17.72 30.78 -1.03 -1.11 -0.83 20.98 17.72 30.78 -1.45 -1.59 -1.21 StruPPi 101
102 Poing 20.98 16.57 29.99 -1.03 -1.26 -0.91 27.59 23.56 35.96 -0.78 -0.83 -0.69 Poing 102
103 FOLDpro 20.69 19.54 22.48 -1.06 -0.88 -1.64 21.84 19.73 25.96 -1.36 -1.33 -1.70 FOLDpro 103
104 PS2−manual 20.69 18.58 32.84 -1.06 -1.00 -0.63 39.66 35.44 41.48 0.43 0.72 -0.14 PS2−manual 104
105 igor 20.11 18.01 26.70 -1.11 -1.08 -1.23 20.11 18.01 26.70 -1.53 -1.55 -1.62 igor 105
106 FUGUE_KM 20.11 17.15 26.99 -1.11 -1.19 -1.20 30.46 27.20 30.58 -0.50 -0.35 -1.23 FUGUE_KM 106
107 FrankensteinLong 19.83 16.57 28.82 -1.14 -1.26 -1.02 47.41 37.64 54.67 1.21 1.01 1.19 FrankensteinLong 107
108 3DShot2 19.83 16.38 25.70 -1.14 -1.28 -1.33 19.83 16.38 25.70 -1.56 -1.76 -1.72 3DShot2 108
109 SAM−T06−server 19.54 18.58 25.41 -1.17 -1.00 -1.36 34.48 28.74 30.30 -0.09 -0.15 -1.26 SAM−T06−server 109
110 RANDOM 19.25 16.91 19.25 -1.20 -1.22 -1.96 19.25 16.91 19.25 -1.62 -1.69 -2.37 RANDOM 110
111 CpHModels 19.25 15.61 27.39 -1.20 -1.38 -1.16 19.25 15.61 27.39 -1.62 -1.86 -1.55 CpHModels 111
112 PSI 19.25 13.89 30.29 -1.20 -1.60 -0.88 32.18 28.35 48.15 -0.32 -0.20 0.53 PSI 112
113 MUFOLD−Server 18.97 16.48 26.09 -1.23 -1.27 -1.29 29.31 24.52 38.94 -0.61 -0.70 -0.39 MUFOLD−Server 113
114 schenk−torda−server 18.68 15.42 20.99 -1.25 -1.41 -1.79 19.25 18.49 24.23 -1.62 -1.49 -1.87 schenk−torda−server 114
115 IBT_LT 18.39 16.09 20.56 -1.28 -1.32 -1.83 18.39 16.09 20.56 -1.71 -1.80 -2.24 IBT_LT 115
116 forecast 18.39 14.85 24.68 -1.28 -1.48 -1.43 22.99 20.21 25.37 -1.25 -1.26 -1.76 forecast 116
117 mahmood−torda−server 18.39 14.65 18.77 -1.28 -1.50 -2.01 18.39 16.00 24.52 -1.71 -1.81 -1.84 mahmood−torda−server 117
118 GS−MetaServer2 18.10 14.94 10.62 -1.31 -1.47 -2.81 19.54 16.09 10.65 -1.59 -1.80 -3.24 GS−MetaServer2 118
119 GeneSilicoMetaServer 18.10 14.94 10.62 -1.31 -1.47 -2.81 19.54 16.09 10.65 -1.59 -1.80 -3.24 GeneSilicoMetaServer 119
120 pipe_int 17.82 15.71 24.24 -1.34 -1.37 -1.47 17.82 15.71 24.24 -1.76 -1.85 -1.87 pipe_int 120
121 Frankenstein 17.82 15.52 24.63 -1.34 -1.39 -1.43 24.71 21.65 32.27 -1.07 -1.08 -1.06 Frankenstein 121
122 Pushchino 16.95 14.46 10.04 -1.42 -1.53 -2.86 16.95 14.46 10.04 -1.85 -2.01 -3.30 Pushchino 122
123 OLGAFS 16.38 16.09 15.25 -1.48 -1.32 -2.35 19.83 17.34 19.66 -1.56 -1.64 -2.33 OLGAFS 123
124 TWPPLAB 16.38 12.84 26.48 -1.48 -1.74 -1.25 16.38 12.84 26.48 -1.91 -2.22 -1.65 TWPPLAB 124
125 Pcons_local 16.09 14.37 24.09 -1.51 -1.54 -1.49 25.00 23.28 24.09 -1.04 -0.86 -1.89 Pcons_local 125
126 DelCLab 16.09 14.27 22.19 -1.51 -1.55 -1.67 22.41 20.50 23.64 -1.30 -1.23 -1.93 DelCLab 126
127 panther_server 15.52 13.89 22.08 -1.56 -1.60 -1.68 15.52 13.89 22.08 -2.00 -2.09 -2.09 panther_server 127
128 SAM−T02−server 15.52 11.69 17.20 -1.56 -1.88 -2.16 22.99 17.82 26.16 -1.25 -1.58 -1.68 SAM−T02−server 128
129 rehtnap 6.90 4.79 0.00 -2.41 -2.76 -3.85 6.90 5.27 0.00 -2.86 -3.21 -4.31 rehtnap 129
130 AMU−Biology                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 AMU−Biology 130
131 Abagyan                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 Abagyan 131
132 BHAGEERATH                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 BHAGEERATH 132
133 CBSU                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 CBSU 133
134 FEIG_REFINE                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 FEIG_REFINE 134
135 Fiser−M4T                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 Fiser−M4T 135
136 HCA                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 HCA 136
137 JIVE08                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 JIVE08 137
138 LEE−SERVER                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 LEE−SERVER 138
139 Linnolt−UH−CMB                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 Linnolt−UH−CMB 139
140 NIM2                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 NIM2 140
141 Nano_team                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 Nano_team 141
142 NirBenTal                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 NirBenTal 142
143 PHAISTOS                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 PHAISTOS 143
144 PZ−UAM                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 PZ−UAM 144
145 ProtAnG                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 ProtAnG 145
146 RPFM                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 RPFM 146
147 ShakAbInitio                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 ShakAbInitio 147
148 TsaiLab                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 TsaiLab 148
149 UCDavisGenome                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 UCDavisGenome 149
150 Wolfson−FOBIA                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 Wolfson−FOBIA 150
151 YASARA                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 YASARA 151
152 YASARARefine                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 YASARARefine 152
153 Zhou−SPARKS                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 Zhou−SPARKS 153
154 dill_ucsf                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 dill_ucsf 154
155 dill_ucsf_extended                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 dill_ucsf_extended 155
156 fais@hgc                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 fais@hgc 156
157 jacobson                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 jacobson 157
158 mti                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 mti 158
159 mumssp                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 mumssp 159
160 psiphifoldings                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 psiphifoldings 160
161 ricardo                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 ricardo 161
162 rivilo                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 rivilo 162
163 sessions                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 sessions 163
164 test_http_server_01                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 test_http_server_01 164
165 tripos_08                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 tripos_08 165
166 xianmingpan                   -1.20 -1.22 -1.96                   -1.62 -1.69 -2.37 xianmingpan 166


1) Agrawal V. & Kishan RK. (2001) "Functional evolution of two subtly different (similar) folds." BMC Struct Biol 1:5, PMID: 11782293