T0467

Human/Server Targets
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T0467

hypothetical membrane-associated protein BC4932 from Bacillus cereus

Target type: Human/Server

Target sequence:

>T0467 BcR97A, Bacillus cereus, 97 residues
MDLNRMGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKDGKEKELEFTAQKNLRKEAFLRVYHSDKKGVSAWEEVKKDELPAKVKEKLGVK

Structure:
Method: NMR
Determined by: NESG
PDB ID: 2k5q

jumping through 467 NMR models
Jumping through 20 NMR models of 2k5q

all 20 467 NMR models
All 20 superimposed NMR models of 2k5q

PyMOL of 2k5q

Domains:  PyMOL of domains

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

Structure classification:

OB-fold. 5-stranded β-barrel, partly open between the 3rd and the 5th β-strands. The five strands are shown in the ribbon diagram below as dark blue, cyan-green, lime-green, yellow and orange. In addition to the 5-stranded OB-core, this structure is elaborated with the long insertion between β-strands 1 and 2 housing an α-helix, and a C-terminal α-helix.

2k5q_1:7-97 cartoon
Cartoon diagram of T0467: 2k5q model 1 residues 7-97

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 = d1quqb_ b.40.4.3 Replication protein A 14 KDa (RPA14) subun
length=114  filtered_length=112  Neff=10.250  Smith-Waterman score = 38  E-value = 2.43e+01
QUERY         38     KLTGFDKDGKEKELEFTAQKNLRKEAFLRV==YHSDKKGVSAWEEVK  82
CONSENSUS_1   37     KLKGYDKDGKEKEVKFTADKKLKKGAYLKL==YVNKGKGVKSWEEVK  81
                     +L + + DG++ +V+++ + +L +G+Y+++  +VN++ +++  + ++
CONSENSUS_2   38     TLTLSSGDGGNVTVELNPPLDLEIGGYVEVIGKVNGDLTIRALSYID  84
d1quqb_       38     MFILSDGEGKNGTIELMEPLDEEISGIVEVVGRVTAKATILCTSYVQ  84

However, this is the hit #24 in the total list of hits and its E-value is around 25 (which indicates BTW how good COMPASS E-value estimate is), so it can hardy be called statistically significant. Moreover, SH3 domain proteins were found by COMPASS prior to this hit. Nevertheless, 9 consensus match residues in the above alignment shown as "dots" on the two OB-fold structures map to structurally equivalent positions validating the COMPASS alignment:

2k5q_1:7-97
T0467: 2k5q model 1 residues 7-97

1quq_B:23-104
RPA14: 1quq chain B residues 23-104

According to structure, proteins from 'Nucleic acid - binding' superfamily are also most similar to T0467, and those include phage ssDNA - binding proteins with an open barrel.

Target sequence - PDB file inconsistencies:

NMR models contain the C-terminal His-tag residues 98-LEHHHHHH-105, not present in the target sequence. This regions was removed from NMR models due to disorder anyway.

T0467    2k5q.pdb    T0467.pdb    PyMOL    PyMOL of domains    

T0467    1 MDLNRMGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKDGKEKELEFTAQKNLRKEAFLRVYHSDKKGVSAWEEVKKDELPAKVKEKLGVK-------- 97
           *******|||||||||||||||||||***|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||***~~~~~~~~
2k5qA    1 MDLNRMGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKDGKEKELEFTAQKNLRKEAFLRVYHSDKKGVSAWEEVKKDELPAKVKEKLGVKLEHHHHHH 105

Residue change log: remove 98-LEHHHHHH-105 as it is not present in target sequence; remove 1-MDLNRMG-7, 27-DNG-29, 95-GVK-97 by 3.5Å SD cutoff;

Single domain protein: target 8-26, 30-94 ; pdb 8-26, 30-94

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                                              
T0467         1  M---------------------------------------DLNR--MGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKD---GKEKELEFTAQ-----KNLRKEAFLRVYHSDK---------KGVSAWEEVKKDELPAKVKEKLGVK------------------------------------   97
T0468         1  M--ERA----------------------------------SLNR--IGKDVYYMQIKGEGTIEKVDG-----RNLRNYTLPAYDED---GVKKQITFRSTKKENDHKLNKYAFLRLYVDQDDNSKNEISSIEVKSYEEIQKADLPEKVKDKFTIK------------------------------------  109
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 T0468:

PSIPRED  ------------EEEEEEE---EEEE-------EEEEEEEEEEEE-----EEEEEEE--------------EEEEEE--------------EEEEEEE------HHHHHHH---
T0467    MD---LNRMGKDEYYVQITVDGKEVHSKADNGQKYKDYEYKLTGFDKDGKEKELEFTAQK-----NLRKEAFLRVYHSDK---------KGVSAWEEVKKDELPAKVKEKLGVK
T0468    MERASLNRIGKDVYYMQIKGEGTIEKV-----DGRNLRNYTLPAYDEDGVKKQITFRSTKKENDHKLNKYAFLRLYVDQDDNSKNEISSIEVKSYEEIQKADLPEKVKDKFTIK
PSIPRED  ------------EEEEEE----EEE-----------EEEEEEEEE-----EEEEEEE--------------EEEEEEE------------EEEEHHH--HHH--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, and incorrectly provides SH3-like predictions. 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.

2k5q_1:64-97
T0467 OB-fold C-terminal fragment:
2k5q model 1 residues 64-97

2bf4_1:30-64
Sso7d SH3-fold C-terminal fragment:
2bf4 chain A residues 30-64

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. 

2k5q   64 FLRVYHSDKKGVSAWEEVKKDELPAKVKEKLGV 96
2bf4_A 30 ISFTYDEGG-GKTGRGAVSEKDAPKELLQMLEK 61
          EEEEEEEE  EEEEEEEEHHHH HHHHHHHHHH  

Therefore it is not surprising that servers find this similarity. 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 T0467. In addition, the surface of the hairpin buried in SH3 fold is exposed in T0467. These inconsistencies in hydrophobic patterns are very suggestive of global structural differences:

2k5q_1:7-97
T0467 OB-fold: 2k5q model 1 residues 7-97

2bf4_A
Sso7d SH3-fold: 2bf4 chain A

DALI-LITE does not see this local similarity, but aligns the central 3-stranded meander β-sheet in two proteins (shown in the back on the images above: blue-cyan-green in T0467, and green-yellow in Sso7d), 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 T0467 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:

T0467:pdb 8-94:seq 8-94:FR;   alignment

distribution of first scores
First models for T0467: Gaussian kernel density estimation for GDT-TS scores of the first server models, plotted at various bandwidths (=standard deviations). The GDT-TS scores are shown as a spectrum along the horizontal axis: each bar represents first server model. The bars are colored green, gray and black for top 10, bottom 25% and the rest of servers. The family of curves with varying bandwidth is shown. Bandwidth varies from 0.3 to 8.2 GDT-TS % units with a step of 0.1, which corresponds to the color ramp from magenta through blue to cyan. Thicker curves: red, yellow-framed brown and black, correspond to bandwidths 1, 2 and 4 respectively.

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 #
T0467 T0467 T0467 T0467
First score First Z-score Best score Best Z-score
1 DBAKER 62.80 57.04 72.96 3.91 4.43 3.30 67.86 59.82 76.41 3.44 3.65 3.07 DBAKER 1
2 Jones−UCL 53.27 44.34 60.79 2.71 2.55 2.09 53.27 44.34 60.79 1.88 1.71 1.61 Jones−UCL 2
3 MUFOLD−MD 50.30 41.77 61.34 2.34 2.17 2.15 54.46 48.31 61.34 2.01 2.21 1.66 MUFOLD−MD 3
4 McGuffin 50.00 42.86 53.52 2.30 2.34 1.38 50.30 42.86 54.23 1.56 1.52 1.00 McGuffin 4
5 METATASSER 50.00 39.48 63.02 2.30 1.84 2.31 50.00 39.48 63.02 1.53 1.10 1.82 METATASSER 5
6 MULTICOM 48.21 42.66 53.94 2.08 2.31 1.42 48.21 42.66 54.37 1.34 1.50 1.01 MULTICOM 6
7 Chicken_George 47.92 45.34 46.73 2.04 2.70 0.70 53.27 45.34 57.53 1.88 1.84 1.31 Chicken_George 7
8 mariner1 45.83 39.68 42.06 1.78 1.87 0.24 55.95 47.62 58.75 2.16 2.12 1.42 mariner1 8
9 Bates_BMM 45.83 37.30 51.13 1.78 1.52 1.14 45.83 37.70 51.70 1.08 0.88 0.76 Bates_BMM 9
10 3DShotMQ 45.24 39.09 50.36 1.71 1.78 1.06 45.24 39.09 50.36 1.02 1.05 0.63 3DShotMQ 10
11 SAMUDRALA 44.34 38.39 52.27 1.59 1.68 1.25 45.24 39.88 54.32 1.02 1.15 1.00 SAMUDRALA 11
12 Zhang−Server 43.45 35.71 54.37 1.48 1.28 1.46 47.92 41.77 56.23 1.30 1.39 1.18 Zhang−Server 12
13 A−TASSER 43.16 38.00 50.06 1.45 1.62 1.03 57.74 51.98 64.52 2.36 2.67 1.96 A−TASSER 13
14 Handl−Lovell 42.86 37.50 50.68 1.41 1.55 1.09 42.86 37.50 53.84 0.76 0.85 0.96 Handl−Lovell 14
15 LEE 42.26 36.11 51.16 1.33 1.34 1.14 42.26 36.11 51.16 0.70 0.68 0.71 LEE 15
16 Zhang 42.26 35.71 56.81 1.33 1.28 1.70 45.54 40.77 57.68 1.05 1.26 1.32 Zhang 16
17 MULTICOM−CLUSTER 41.96 34.42 51.09 1.30 1.09 1.14 50.00 42.86 54.01 1.53 1.52 0.98 MULTICOM−CLUSTER 17
18 fais@hgc 41.67 31.15 51.45 1.26 0.61 1.17 41.67 34.92 53.01 0.64 0.53 0.88 fais@hgc 18
19 forecast 41.37 33.13 43.07 1.22 0.90 0.34 41.37 34.62 43.11 0.60 0.49 -0.05 forecast 19
20 MUProt 41.07 34.52 50.95 1.18 1.11 1.12 50.30 42.56 54.59 1.56 1.49 1.03 MUProt 20
21 TASSER 41.07 32.54 54.52 1.18 0.81 1.47 45.24 35.52 64.52 1.02 0.60 1.96 TASSER 21
22 Bilab−UT 40.18 31.65 45.90 1.07 0.68 0.62 40.18 32.64 45.90 0.48 0.24 0.22 Bilab−UT 22
23 GS−KudlatyPred 39.88 31.55 48.75 1.03 0.67 0.90 39.88 31.55 48.75 0.44 0.10 0.48 GS−KudlatyPred 23
24 Hao_Kihara 39.58 35.22 47.40 1.00 1.21 0.77 39.58 35.22 48.55 0.41 0.56 0.46 Hao_Kihara 24
25 AMU−Biology 39.58 33.53 52.46 1.00 0.96 1.27 39.58 35.02 52.46 0.41 0.54 0.83 AMU−Biology 25
26 MULTICOM−REFINE 39.29 34.52 50.31 0.96 1.11 1.06 49.41 41.07 54.28 1.46 1.30 1.00 MULTICOM−REFINE 26
27 JIVE08 38.99 35.22 50.59 0.92 1.21 1.09 38.99 35.32 50.59 0.35 0.58 0.66 JIVE08 27
28 3DShot1 38.99 30.06 46.85 0.92 0.45 0.72 38.99 30.06 46.85 0.35 -0.08 0.30 3DShot1 28
29 SAINT1 38.69 32.04 47.02 0.88 0.74 0.73 38.69 32.04 47.02 0.32 0.16 0.32 SAINT1 29
30 PSI 38.09 33.33 47.62 0.81 0.93 0.79 38.99 33.63 47.74 0.35 0.36 0.39 PSI 30
31 ABIpro 37.80 30.46 46.47 0.77 0.51 0.68 38.39 31.05 46.55 0.28 0.04 0.28 ABIpro 31
32 keasar 36.31 31.35 46.99 0.59 0.64 0.73 36.91 33.04 49.29 0.13 0.29 0.53 keasar 32
33 Sasaki−Cetin−Sasai 36.31 30.95 49.11 0.59 0.58 0.94 36.31 30.95 49.11 0.06 0.03 0.52 Sasaki−Cetin−Sasai 33
34 POEM 36.31 30.16 53.22 0.59 0.46 1.35 47.32 41.17 61.03 1.24 1.31 1.63 POEM 34
35 TJ_Jiang 35.42 29.07 47.10 0.47 0.30 0.74 35.42 29.07 47.11 -0.03 -0.21 0.33 TJ_Jiang 35
36 POEMQA 35.42 28.47 44.96 0.47 0.21 0.53 38.69 32.74 52.94 0.32 0.25 0.88 POEMQA 36
37 MULTICOM−CMFR 35.12 30.95 42.09 0.44 0.58 0.25 35.12 30.95 42.09 -0.07 0.03 -0.14 MULTICOM−CMFR 37
38 KudlatyPredHuman 34.23 27.48 46.89 0.33 0.07 0.72 37.80 30.26 48.22 0.22 -0.06 0.43 KudlatyPredHuman 38
39 BAKER−ROBETTA 33.93 30.66 48.98 0.29 0.54 0.93 39.29 35.71 52.45 0.38 0.63 0.83 BAKER−ROBETTA 39
40 Pcons_dot_net 33.93 30.66 48.98 0.29 0.54 0.93 39.29 35.71 52.45 0.38 0.63 0.83 Pcons_dot_net 40
41 fais−server 33.63 31.25 47.97 0.25 0.62 0.83 40.77 35.22 52.88 0.54 0.56 0.87 fais−server 41
42 mufold 33.63 29.96 48.95 0.25 0.43 0.92 37.50 30.56 48.95 0.19 -0.02 0.50 mufold 42
43 ZicoFullSTPFullData 33.63 28.27 46.75 0.25 0.18 0.71 51.49 43.16 54.01 1.69 1.56 0.98 ZicoFullSTPFullData 43
44 Elofsson 33.33 28.77 42.61 0.21 0.26 0.30 37.20 31.45 44.49 0.16 0.09 0.08 Elofsson 44
45 RBO−Proteus 33.04 27.68 46.57 0.18 0.10 0.69 37.80 33.73 53.81 0.22 0.38 0.96 RBO−Proteus 45
46 BioSerf 32.74 30.26 46.84 0.14 0.48 0.71 45.54 37.60 52.64 1.05 0.86 0.85 BioSerf 46
47 ProteinShop 32.74 30.16 33.98 0.14 0.46 -0.56 33.63 31.05 42.02 -0.23 0.04 -0.15 ProteinShop 47
48 Zico 32.14 30.16 46.54 0.06 0.46 0.69 51.49 43.16 54.01 1.69 1.56 0.98 Zico 48
49 ZicoFullSTP 32.14 30.16 46.54 0.06 0.46 0.69 51.49 43.16 54.01 1.69 1.56 0.98 ZicoFullSTP 49
50 HHpred4 32.14 23.02 37.75 0.06 -0.59 -0.18 32.14 23.02 37.75 -0.39 -0.97 -0.55 HHpred4 50
51 HHpred5 32.14 23.02 37.75 0.06 -0.59 -0.18 32.14 23.02 37.75 -0.39 -0.97 -0.55 HHpred5 51
52 fams−ace2 30.95 27.48 41.40 -0.09 0.07 0.18 50.30 42.36 64.12 1.56 1.46 1.92 fams−ace2 52
53 pro−sp3−TASSER 30.95 27.38 50.86 -0.09 0.05 1.11 46.43 40.87 60.14 1.14 1.27 1.55 pro−sp3−TASSER 53
54 GeneSilico 30.95 25.20 28.14 -0.09 -0.27 -1.13 51.49 44.74 61.02 1.69 1.76 1.63 GeneSilico 54
55 ShakAbInitio 30.95 25.10 43.10 -0.09 -0.28 0.35 33.93 29.27 44.65 -0.19 -0.18 0.10 ShakAbInitio 55
56 3D−JIGSAW_AEP 30.66 27.08 31.78 -0.12 0.01 -0.77 30.66 27.48 32.46 -0.54 -0.41 -1.04 3D−JIGSAW_AEP 56
57 SAM−T08−server 30.36 27.98 41.13 -0.16 0.14 0.15 35.42 27.98 42.89 -0.03 -0.34 -0.07 SAM−T08−server 57
58 MULTICOM−RANK 30.36 26.98 39.31 -0.16 -0.01 -0.03 32.14 30.36 39.85 -0.39 -0.05 -0.35 MULTICOM−RANK 58
59 FFASsuboptimal 30.06 26.29 28.96 -0.20 -0.11 -1.05 30.36 28.18 31.70 -0.58 -0.32 -1.11 FFASsuboptimal 59
60 Sternberg 30.06 22.72 47.80 -0.20 -0.63 0.81 30.06 26.09 47.80 -0.61 -0.58 0.39 Sternberg 60
61 FALCON 29.76 25.40 44.33 -0.24 -0.24 0.47 40.18 34.23 52.20 0.48 0.44 0.81 FALCON 61
62 EB_AMU_Physics 29.76 25.00 34.23 -0.24 -0.30 -0.53 29.76 25.00 34.23 -0.64 -0.72 -0.88 EB_AMU_Physics 62
63 FFASstandard 29.76 24.60 23.21 -0.24 -0.36 -1.62 29.76 25.50 23.21 -0.64 -0.66 -1.91 FFASstandard 63
64 FFASflextemplate 29.76 24.60 23.21 -0.24 -0.36 -1.62 29.76 25.50 23.21 -0.64 -0.66 -1.91 FFASflextemplate 64
65 Phyre2 29.46 27.88 41.31 -0.27 0.13 0.17 29.46 27.88 41.31 -0.67 -0.36 -0.21 Phyre2 65
66 FLOUDAS 29.46 25.79 38.46 -0.27 -0.18 -0.11 33.93 27.98 41.33 -0.19 -0.34 -0.21 FLOUDAS 66
67 MUSTER 29.17 27.38 38.66 -0.31 0.05 -0.09 29.17 27.38 38.66 -0.70 -0.42 -0.46 MUSTER 67
68 HHpred2 29.17 27.18 37.09 -0.31 0.02 -0.25 29.17 27.18 37.09 -0.70 -0.45 -0.61 HHpred2 68
69 SAM−T08−human 29.17 23.81 44.58 -0.31 -0.47 0.49 33.33 29.07 48.95 -0.26 -0.21 0.50 SAM−T08−human 69
70 FAMS−multi 28.87 27.08 39.36 -0.35 0.01 -0.02 30.06 27.08 39.36 -0.61 -0.46 -0.40 FAMS−multi 70
71 FALCON_CONSENSUS 28.87 23.31 48.32 -0.35 -0.55 0.86 29.76 25.40 48.32 -0.64 -0.67 0.44 FALCON_CONSENSUS 71
72 Distill 28.57 25.40 35.67 -0.38 -0.24 -0.39 30.66 27.58 37.63 -0.54 -0.40 -0.56 Distill 72
73 FEIG 28.27 26.49 39.82 -0.42 -0.08 0.02 28.57 26.49 45.29 -0.77 -0.53 0.16 FEIG 73
74 Kolinski 28.27 25.50 35.96 -0.42 -0.22 -0.36 28.87 26.29 35.96 -0.74 -0.56 -0.72 Kolinski 74
75 Pcons_multi 28.27 23.61 35.89 -0.42 -0.50 -0.37 30.06 24.41 39.14 -0.61 -0.79 -0.42 Pcons_multi 75
76 Ozkan−Shell 28.27 22.32 46.84 -0.42 -0.69 0.71 31.55 29.27 47.92 -0.45 -0.18 0.41 Ozkan−Shell 76
77 pipe_int 27.38 25.40 36.75 -0.53 -0.24 -0.28 27.38 25.40 36.75 -0.90 -0.67 -0.64 pipe_int 77
78 PS2−server 27.38 24.80 34.72 -0.53 -0.33 -0.48 30.06 26.69 43.87 -0.61 -0.51 0.03 PS2−server 78
79 PS2−manual 27.38 24.80 34.31 -0.53 -0.33 -0.52 30.06 26.69 43.91 -0.61 -0.51 0.03 PS2−manual 79
80 FUGUE_KM 27.38 24.41 27.22 -0.53 -0.38 -1.23 27.98 25.10 28.02 -0.83 -0.71 -1.46 FUGUE_KM 80
81 3D−JIGSAW_V3 27.08 25.40 32.07 -0.57 -0.24 -0.75 27.08 25.40 32.07 -0.93 -0.67 -1.08 3D−JIGSAW_V3 81
82 keasar−server 26.79 23.11 32.90 -0.61 -0.58 -0.66 26.79 25.30 32.90 -0.96 -0.68 -1.00 keasar−server 82
83 DistillSN 26.79 22.82 34.41 -0.61 -0.62 -0.51 32.14 27.38 39.78 -0.39 -0.42 -0.36 DistillSN 83
84 Pcons_local 26.79 22.42 22.62 -0.61 -0.68 -1.68 26.79 22.42 24.73 -0.96 -1.04 -1.77 Pcons_local 84
85 MUFOLD−Server 26.49 22.72 33.40 -0.65 -0.63 -0.61 29.17 25.59 37.90 -0.70 -0.65 -0.53 MUFOLD−Server 85
86 GS−MetaServer2 26.19 22.62 23.61 -0.68 -0.65 -1.58 30.95 25.20 28.60 -0.51 -0.69 -1.40 GS−MetaServer2 86
87 GeneSilicoMetaServer 26.19 22.62 23.61 -0.68 -0.65 -1.58 30.95 25.20 28.60 -0.51 -0.69 -1.40 GeneSilicoMetaServer 87
88 CpHModels 25.89 21.73 22.87 -0.72 -0.78 -1.66 25.89 21.73 22.87 -1.06 -1.13 -1.94 CpHModels 88
89 FrankensteinLong 25.59 20.24 33.52 -0.76 -1.00 -0.60 31.84 29.66 40.95 -0.42 -0.13 -0.25 FrankensteinLong 89
90 SAM−T06−server 25.30 23.51 31.80 -0.80 -0.52 -0.77 29.17 23.91 31.80 -0.70 -0.86 -1.11 SAM−T06−server 90
91 xianmingpan 25.30 20.14 25.26 -0.80 -1.01 -1.42 25.30 20.14 30.12 -1.12 -1.33 -1.26 xianmingpan 91
92 LOOPP_Server 25.30 18.75 28.95 -0.80 -1.22 -1.05 27.08 24.60 35.19 -0.93 -0.77 -0.79 LOOPP_Server 92
93 MidwayFolding 25.00 21.53 30.93 -0.83 -0.81 -0.86 52.38 44.74 54.06 1.78 1.76 0.98 MidwayFolding 93
94 LevittGroup 25.00 21.03 29.81 -0.83 -0.88 -0.97 25.89 22.72 30.18 -1.06 -1.01 -1.26 LevittGroup 94
95 RAPTOR 25.00 20.64 26.81 -0.83 -0.94 -1.27 52.38 44.74 54.70 1.78 1.76 1.04 RAPTOR 95
96 Wolynes 24.70 19.15 30.62 -0.87 -1.16 -0.89 33.04 28.47 44.46 -0.29 -0.28 0.08 Wolynes 96
97 SMEG−CCP 24.70 18.95 44.11 -0.87 -1.19 0.44 24.70 18.95 44.11 -1.18 -1.48 0.05 SMEG−CCP 97
98 Frankenstein 24.41 23.81 31.39 -0.91 -0.47 -0.81 31.84 29.66 41.30 -0.42 -0.13 -0.22 Frankenstein 98
99 nFOLD3 24.11 18.55 29.08 -0.94 -1.25 -1.04 29.46 25.50 41.24 -0.67 -0.66 -0.22 nFOLD3 99
100 FAMSD 23.81 20.93 28.87 -0.98 -0.90 -1.06 25.89 22.52 32.43 -1.06 -1.03 -1.05 FAMSD 100
101 3DShot2 23.51 20.54 38.10 -1.02 -0.95 -0.15 23.51 20.54 38.10 -1.31 -1.28 -0.51 3DShot2 101
102 Jiang_Zhu 23.21 19.84 29.75 -1.06 -1.06 -0.97 23.21 20.14 29.75 -1.34 -1.33 -1.30 Jiang_Zhu 102
103 MeilerLabRene 23.21 19.44 28.38 -1.06 -1.12 -1.11 25.59 22.42 32.77 -1.09 -1.04 -1.01 MeilerLabRene 103
104 Phyre_de_novo 22.92 20.04 31.22 -1.09 -1.03 -0.83 31.25 27.88 40.21 -0.48 -0.36 -0.32 Phyre_de_novo 104
105 Phragment 22.32 18.35 28.75 -1.17 -1.28 -1.07 24.70 22.72 29.57 -1.18 -1.01 -1.31 Phragment 105
106 POISE 22.32 18.35 39.49 -1.17 -1.28 -0.01 30.95 27.98 39.49 -0.51 -0.34 -0.38 POISE 106
107 mahmood−torda−server 22.32 17.96 26.26 -1.17 -1.33 -1.32 22.32 17.96 26.77 -1.44 -1.60 -1.58 mahmood−torda−server 107
108 Poing 22.02 20.54 31.99 -1.21 -0.95 -0.75 26.79 21.03 37.46 -0.96 -1.22 -0.57 Poing 108
109 SHORTLE 21.43 19.74 25.07 -1.28 -1.07 -1.44 23.21 20.44 25.07 -1.34 -1.29 -1.74 SHORTLE 109
110 mGenTHREADER 21.43 18.06 16.86 -1.28 -1.32 -2.25 21.43 18.06 16.86 -1.53 -1.59 -2.50 mGenTHREADER 110
111 taylor 21.43 16.27 27.25 -1.28 -1.58 -1.22 23.21 20.93 34.72 -1.34 -1.23 -0.83 taylor 111
112 Scheraga 21.13 18.55 30.82 -1.32 -1.25 -0.87 25.59 20.93 33.00 -1.09 -1.23 -0.99 Scheraga 112
113 ACOMPMOD 21.13 18.55 25.84 -1.32 -1.25 -1.36 28.57 23.02 30.43 -0.77 -0.97 -1.23 ACOMPMOD 113
114 3Dpro 21.13 17.56 27.74 -1.32 -1.39 -1.17 21.13 17.56 27.74 -1.57 -1.65 -1.49 3Dpro 114
115 COMA 21.13 16.77 25.21 -1.32 -1.51 -1.42 23.51 20.73 26.17 -1.31 -1.26 -1.63 COMA 115
116 circle 21.13 14.38 25.30 -1.32 -1.86 -1.41 42.56 39.19 49.91 0.73 1.06 0.59 circle 116
117 igor 20.83 18.95 25.69 -1.36 -1.19 -1.38 20.83 18.95 25.69 -1.60 -1.48 -1.68 igor 117
118 Softberry 20.24 19.25 24.52 -1.43 -1.14 -1.49 25.00 21.23 28.71 -1.15 -1.19 -1.39 Softberry 118
119 Pushchino 20.24 18.06 16.23 -1.43 -1.32 -2.31 20.24 18.06 16.23 -1.66 -1.59 -2.56 Pushchino 119
120 COMA−M 20.24 17.46 24.78 -1.43 -1.41 -1.47 21.13 17.46 26.17 -1.57 -1.67 -1.63 COMA−M 120
121 RANDOM 20.05 17.29 20.05 -1.45 -1.43 -1.93 20.05 17.29 20.05 -1.68 -1.69 -2.21 RANDOM 121
122 fleil 19.94 15.18 30.14 -1.47 -1.74 -0.94 22.02 19.05 31.48 -1.47 -1.47 -1.14 fleil 122
123 IBT_LT 19.64 17.26 27.15 -1.51 -1.44 -1.23 19.64 17.26 27.15 -1.72 -1.69 -1.54 IBT_LT 123
124 schenk−torda−server 19.34 14.98 22.17 -1.54 -1.77 -1.72 20.54 17.96 26.89 -1.63 -1.60 -1.57 schenk−torda−server 124
125 StruPPi 18.75 17.76 28.66 -1.62 -1.36 -1.08 18.75 17.76 28.66 -1.82 -1.63 -1.40 StruPPi 125
126 PRI−Yang−KiharA 18.45 17.16 20.08 -1.65 -1.45 -1.93 18.45 17.16 20.08 -1.85 -1.70 -2.20 PRI−Yang−KiharA 126
127 RPFM 18.45 16.67 24.59 -1.65 -1.52 -1.49 18.45 16.67 24.88 -1.85 -1.77 -1.75 RPFM 127
128 OLGAFS 18.16 14.19 13.74 -1.69 -1.89 -2.56 18.75 14.58 14.81 -1.82 -2.03 -2.70 OLGAFS 128
129 DelCLab 17.56 15.68 22.00 -1.77 -1.67 -1.74 18.16 16.07 22.02 -1.88 -1.84 -2.02 DelCLab 129
130 FOLDpro 17.26 15.28 19.65 -1.80 -1.73 -1.97 22.02 18.55 23.25 -1.47 -1.53 -1.91 FOLDpro 130
131 rehtnap 17.26 14.88 6.50 -1.80 -1.79 -3.27 17.26 16.96 6.50 -1.98 -1.73 -3.48 rehtnap 131
132 TWPPLAB 17.26 14.78 20.93 -1.80 -1.80 -1.85 17.26 14.78 20.93 -1.98 -2.00 -2.12 TWPPLAB 132
133 huber−torda−server 16.07 14.09 17.15 -1.95 -1.91 -2.22 25.89 21.53 27.39 -1.06 -1.16 -1.52 huber−torda−server 133
134 SAM−T02−server 13.99 13.10 6.78 -2.21 -2.05 -3.25 26.19 21.63 20.48 -1.02 -1.14 -2.17 SAM−T02−server 134
135 Abagyan                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 Abagyan 135
136 BHAGEERATH                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 BHAGEERATH 136
137 CBSU                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 CBSU 137
138 FEIG_REFINE                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 FEIG_REFINE 138
139 Fiser−M4T                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 Fiser−M4T 139
140 HCA                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 HCA 140
141 LEE−SERVER                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 LEE−SERVER 141
142 Linnolt−UH−CMB                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 Linnolt−UH−CMB 142
143 NIM2                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 NIM2 143
144 Nano_team                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 Nano_team 144
145 NirBenTal                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 NirBenTal 145
146 PHAISTOS                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 PHAISTOS 146
147 PZ−UAM                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 PZ−UAM 147
148 ProtAnG                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 ProtAnG 148
149 TsaiLab                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 TsaiLab 149
150 UCDavisGenome                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 UCDavisGenome 150
151 Wolfson−FOBIA                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 Wolfson−FOBIA 151
152 YASARA                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 YASARA 152
153 YASARARefine                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 YASARARefine 153
154 Zhou−SPARKS                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 Zhou−SPARKS 154
155 dill_ucsf                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 dill_ucsf 155
156 dill_ucsf_extended                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 dill_ucsf_extended 156
157 jacobson                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 jacobson 157
158 mti                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 mti 158
159 mumssp                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 mumssp 159
160 panther_server                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 panther_server 160
161 psiphifoldings                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 psiphifoldings 161
162 ricardo                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 ricardo 162
163 rivilo                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 rivilo 163
164 sessions                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 sessions 164
165 test_http_server_01                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 test_http_server_01 165
166 tripos_08                   -1.45 -1.43 -1.93                   -1.68 -1.69 -2.21 tripos_08 166

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