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Table 3 Cumulative observed model quality scores for each MQAP (TS1 and AL1 models)

From: Benchmarking consensus model quality assessment for protein fold recognition

  TM-score MaxSub GDT Combined
Maximum MQAP Score 62.30 52.98 56.25 57.18
Zhang-Server_TS1 58.21 48.77 52.03 53.00
3D-Jury 58.02 48.32 51.96 52.77
Pcons* 55.55 47.00 50.08 50.87
LEE* 55.20 45.77 49.60 50.19
ModFOLD 55.39 45.47 49.62 50.16
HHpred2_TS1 54.95 45.22 49.16 49.78
Pcons6_TS1 54.67 45.08 48.52 49.42
Pmodeller6_TS1 54.77 44.76 48.73 49.42
ROBETTA_TS1 54.92 44.43 48.85 49.40
CIRCLE_TS1 54.69 44.59 48.49 49.26
HHpred3_TS1 54.33 44.76 48.52 49.20
BayesHH_TS1 54.39 44.33 48.41 49.04
MetaTasser_TS1 55.17 43.80 48.15 49.04
HHpred1_TS1 54.18 44.48 48.04 48.90
UNI-EID_expm_TS1 54.06 44.58 47.95 48.86
ModSSEA 54.30 43.88 48.35 48.84
beautshot_TS1 54.37 44.25 47.75 48.79
FAMSD_TS1 54.07 44.08 48.05 48.73
PROQ* 53.47 44.50 48.15 48.71
RAPTOR-ACE_TS1 54.05 43.80 47.69 48.52
FAMS_TS1 53.84 43.70 47.84 48.46
SP3_TS1 53.51 43.48 47.41 48.13
SP4_TS1 53.44 43.19 47.11 47.91
shub_TS1 53.35 43.31 46.87 47.84
RAPTOR_TS1 53.48 42.88 47.16 47.84
UNI-EID_bnmx_TS1 52.33 43.72 46.88 47.64
beautshotbase_TS1 52.46 43.05 46.59 47.37
RAPTORESS_TS1 53.17 42.44 46.46 47.36
FUNCTION_TS1 52.75 42.59 46.57 47.30
SPARKS2_TS1 52.47 42.49 46.19 47.05
PROQ-LG 51.49 43.04 46.43 46.99
3Dpro_TS1 51.81 42.16 46.34 46.77
FOLDpro_TS1 51.77 42.06 46.10 46.64
GeneSilicoMetaServer_TS1 51.75 42.09 45.87 46.57
UNI-EID_sfst_AL1.pdb 50.39 42.55 45.37 46.10
PROTINFO_TS1 51.28 41.36 45.60 46.08
Ma-OPUS-server_TS1 51.23 40.96 45.30 45.83
SAM_T06_server_TS1 51.35 40.66 45.12 45.71
PROQ-MX 49.89 41.60 44.89 45.46
PROTINFO-AB_TS1 50.64 40.65 44.65 45.32
Phyre-2_TS1 50.26 40.32 44.38 44.99
ROKKY_TS1 49.66 40.42 44.16 44.75
mGen-3D_TS1 49.29 40.15 44.22 44.55
Bilab-ENABLE_TS1 49.59 39.16 43.26 44.00
SAM-T02_AL1.pdb 48.13 40.12 43.03 43.76
LOOPP_TS1 48.44 38.64 42.73 43.27
FUGUE_AL1.pdb 47.55 38.79 42.53 42.96
nFOLD_TS1 47.40 38.46 41.95 42.60
keasar-server_TS1 47.84 38.20 41.59 42.54
Phyre-1_TS1 46.87 38.16 41.63 42.22
MODCHECK 47.03 37.76 41.65 42.15
NN_PUT_lab_TS1 46.95 37.72 41.26 41.98
CaspIta-FOX_TS1 46.53 37.47 41.01 41.67
FUGMOD_TS1 46.37 37.42 41.10 41.63
FORTE1_AL1.pdb 46.51 37.06 40.66 41.41
FORTE2_AL1.pdb 46.30 36.89 40.56 41.25
3D-JIGSAW_POPULUS_TS1 44.74 35.44 39.34 39.84
karypis.srv_TS1 44.43 35.20 38.95 39.53
3D-JIGSAW_RECOM_TS1 43.70 35.55 38.84 39.36
3D-JIGSAW_TS1 43.53 34.50 38.37 38.80
SAM-T99_AL1.pdb 42.60 35.81 37.64 38.69
karypis.srv.2_TS1 42.77 33.54 37.50 37.94
Huber-Torda-Server_TS1 41.78 34.40 37.21 37.80
forecast-s_AL1.pdb 41.00 33.38 36.48 36.95
Distill_TS1 39.75 27.26 31.94 32.98
Ma-OPUS-server2_TS1 33.35 26.75 29.77 29.96
panther2_TS1 28.87 23.67 25.85 26.13
CPHmodels_TS1 27.75 23.49 24.55 25.26
Frankenstein_TS1 23.55 17.66 20.33 20.52
gtg_AL1.pdb 20.55 16.66 17.81 18.34
ABIpro_TS1 21.88 12.35 17.45 17.22
MIG_FROST_AL1.pdb 16.68 12.11 14.75 14.51
FPSOLVER-SERVER_TS1 14.91 6.78 10.97 10.89
karypis.srv.4_TS1 14.71 6.55 10.66 10.64
POMYSL_TS1 9.64 6.00 8.35 8.00
panther3_TS1 5.75 4.58 5.05 5.12
MIG_FROST_FLEX_AL1.pdb 1.05 0.97 1.07 1.03
  1. Results in bold indicate the cumulative observed model quality scores of the top ranked models for each target (Σm) obtained by using each MQAP method to rank the top models from all fold recognition servers. The maximum achievable MQAP score – obtained by consistently selecting the best model for each target – is also highlighted. All other results are based on the cumulative scores of the TS1 or AL1 models from each fold recognition server taking part in the automated category at CASP7. Each column indicates the method for measuring the observed model quality. Scores are sorted by the combined observed model quality. *The MQAP scores for these methods were downloaded from CASP7 website; all other MQAP methods were run in house during the CASP7 experiment. †MQAP methods which rely on the comparison of multiple models or additional information from multiple servers; all other methods are capable of producing a single score based on a single model.