Home Research Services Publications People Teaching Job Opening News Lab Only
Online Services

I-TASSER QUARK LOMETS COACH COFACTOR MUSTER SEGMER FG-MD ModRefiner REMO SPRING COTH BSpred SVMSEQ ANGLOR BSP-SLIM SAXSTER ThreaDom EvoDesign GPCR-I-TASSER BindProf BindProfX ResQ IonCom STRUM

TM-score TM-align MMalign NWalign EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot I-TASSER-MR

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP TM-fold DECOYS POTENTIAL RW HPSF CASP7 CASP8 CASP9 CASP10 CASP11 CASP12


QUARK Decoy Set

This page contains the decoys of 145 non-homologous small proteins, together with the models selected by the SPICKER clustering program. The backbone structures were generated by the QUARK ab initio modeling; the full-atomic models of the best decoy and the closc model were built by the ModRefiner program.
Explanations:

ID Native Length Decoy_pdb (#) Decoy_Spicker Best_decoy (RMSD/TM) Closc (RMSD/TM)
3CHBD native 103 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.00/0.322) Closc.pdb (13.57/0.244)
1WN2A native 118 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.60/0.411) Closc.pdb (13.09/0.282)
1YKUA native 132 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.80/0.760) Closc.pdb (  5.25/0.501)
1WXCB native 72 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.44/0.396) Closc.pdb (11.84/0.285)
1UFYA native 121 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.23/0.415) Closc.pdb (12.55/0.335)
2OFCA native 141 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.89/0.376) Closc.pdb (  9.76/0.319)
2J9WA native 101 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.82/0.722) Closc.pdb (  6.06/0.463)
1T6UA native 117 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.75/0.800) Closc.pdb (  4.41/0.612)
2FCWA native 106 Decoy_pdb (5000) Decoy_spicker Best_decoy (  1.45/0.881) Closc.pdb (  3.68/0.798)
2NMLA native 100 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.57/0.465) Closc.pdb (11.76/0.276)
2IP6A native 87 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.25/0.755) Closc.pdb (  4.68/0.527)
1J3WA native 134 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.77/0.413) Closc.pdb (14.08/0.285)
1NLQA native 105 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.14/0.351) Closc.pdb (  9.25/0.341)
2CHHA native 113 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.82/0.279) Closc.pdb (10.89/0.324)
1MN8A native 95 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.66/0.403) Closc.pdb (12.10/0.300)
2JEKA native 140 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.04/0.352) Closc.pdb (13.78/0.295)
1N8VA native 101 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.91/0.543) Closc.pdb (11.70/0.334)
1U84A native 81 Decoy_pdb (5000) Decoy_spicker Best_decoy (  1.92/0.788) Closc.pdb (  3.80/0.539)
2V33A native 91 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.85/0.275) Closc.pdb (10.72/0.216)
1W53A native 84 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.99/0.677) Closc.pdb (11.53/0.389)
1UGIA native 83 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.20/0.535) Closc.pdb (  6.32/0.499)
1O82A native 70 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.08/0.532) Closc.pdb (  7.45/0.423)
1OK0A native 74 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.10/0.235) Closc.pdb (12.90/0.181)
1KA8A native 100 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.14/0.334) Closc.pdb (12.62/0.233)
2O42A native 133 Decoy_pdb (5000) Decoy_spicker Best_decoy (13.23/0.272) Closc.pdb (19.94/0.236)
1XZQB native 117 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.08/0.360) Closc.pdb (12.61/0.291)
1V14A native 132 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.25/0.373) Closc.pdb (12.43/0.309)
1OCZE native 109 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.02/0.698) Closc.pdb (  4.93/0.520)
2R41D native 102 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.99/0.365) Closc.pdb (15.65/0.258)
1IS7K native 84 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.36/0.343) Closc.pdb (12.70/0.225)
1XPXA native 144 Decoy_pdb (5000) Decoy_spicker Best_decoy (11.21/0.263) Closc.pdb (20.11/0.284)
1MHDA native 123 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.83/0.462) Closc.pdb (10.72/0.261)
1VASA native 137 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.91/0.392) Closc.pdb (13.47/0.279)
1JC7A native 129 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.49/0.265) Closc.pdb (16.50/0.219)
2BSEA native 107 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.97/0.258) Closc.pdb (14.07/0.270)
2FIOB native 113 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.22/0.296) Closc.pdb (13.69/0.269)
1H4LD native 147 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.97/0.513) Closc.pdb (11.56/0.398)
1CF7B native 82 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.42/0.591) Closc.pdb (  6.55/0.497)
2O26A native 144 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.96/0.310) Closc.pdb (16.90/0.238)
1HL6D native 143 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.90/0.365) Closc.pdb (14.77/0.283)
2D5RB native 116 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.97/0.449) Closc.pdb (13.81/0.293)
2J4BB native 133 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.60/0.557) Closc.pdb (17.12/0.359)
1JSGA native 111 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.45/0.392) Closc.pdb (13.63/0.262)
2HDIB native 103 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.84/0.309) Closc.pdb (14.59/0.207)
2BHMA native 134 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.28/0.382) Closc.pdb (14.24/0.309)
2PT7G native 145 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.84/0.359) Closc.pdb (13.71/0.369)
2YX8A native 79 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.90/0.508) Closc.pdb (10.31/0.374)
1CQAA native 123 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.61/0.500) Closc.pdb (  7.70/0.426)
2GJVA native 136 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.79/0.422) Closc.pdb (18.39/0.251)
2E79A native 108 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.07/0.398) Closc.pdb (12.00/0.323)
1QYND native 136 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.23/0.489) Closc.pdb (17.88/0.284)
2GWFB native 121 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.08/0.271) Closc.pdb (14.01/0.289)
1SMPI native 100 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.03/0.372) Closc.pdb (12.17/0.297)
1E2AA native 102 Decoy_pdb (5000) Decoy_spicker Best_decoy (  1.79/0.838) Closc.pdb (  2.66/0.767)
2QVTA native 113 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.44/0.245) Closc.pdb (16.34/0.183)
2G38C native 76 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.33/0.493) Closc.pdb (  8.97/0.494)
1QC7A native 101 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.64/0.762) Closc.pdb (12.55/0.341)
1B4BA native 71 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.83/0.645) Closc.pdb (  7.49/0.337)
1V1JA native 150 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.69/0.350) Closc.pdb (10.77/0.309)
2BL7A native 77 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.48/0.608) Closc.pdb (10.52/0.287)
1IM3D native 95 Decoy_pdb (5000) Decoy_spicker Best_decoy (11.30/0.262) Closc.pdb (14.25/0.208)
1BG8A native 76 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.82/0.433) Closc.pdb (12.49/0.240)
2QYAA native 115 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.21/0.413) Closc.pdb (11.70/0.345)
1IPIA native 114 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.29/0.550) Closc.pdb (  7.85/0.417)
1K3BA native 119 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.01/0.370) Closc.pdb (14.85/0.303)
2RCFB native 81 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.82/0.327) Closc.pdb (  9.19/0.266)
1J1VA native 92 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.53/0.723) Closc.pdb (  6.76/0.555)
1XEQA native 89 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.80/0.372) Closc.pdb (  8.60/0.342)
2QM2B native 112 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.68/0.472) Closc.pdb (11.41/0.289)
3BJOA native 102 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.58/0.364) Closc.pdb (12.26/0.275)
2H5ND native 123 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.62/0.362) Closc.pdb (11.49/0.334)
1PZWA native 80 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.56/0.488) Closc.pdb (11.30/0.364)
1R7LB native 109 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.81/0.462) Closc.pdb (  7.50/0.402)
1Y96B native 85 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.81/0.369) Closc.pdb (13.25/0.333)
2CZVD native 119 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.99/0.388) Closc.pdb (13.41/0.354)
2B91A native 129 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.32/0.337) Closc.pdb (15.75/0.255)
1LDDA native 74 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.07/0.599) Closc.pdb (10.79/0.353)
2GYBT native 83 Decoy_pdb (5000) Decoy_spicker Best_decoy (  1.08/0.924) Closc.pdb (  1.43/0.867)
2J6ZA native 86 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.33/0.645) Closc.pdb (11.66/0.398)
1NZEA native 112 Decoy_pdb (5000) Decoy_spicker Best_decoy (  1.80/0.862) Closc.pdb (  4.16/0.786)
1Y71B native 110 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.36/0.406) Closc.pdb (10.81/0.337)
2O4TA native 90 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.62/0.707) Closc.pdb (  5.67/0.567)
2V94B native 91 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.33/0.612) Closc.pdb (  4.93/0.468)
1STMA native 141 Decoy_pdb (5000) Decoy_spicker Best_decoy (13.07/0.215) Closc.pdb (16.55/0.203)
1R75A native 110 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.79/0.371) Closc.pdb (16.13/0.205)
1MWPA native 96 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.60/0.285) Closc.pdb (12.61/0.300)
1V54H native 79 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.80/0.586) Closc.pdb (  6.26/0.532)
2IGPA native 114 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.56/0.493) Closc.pdb (11.29/0.388)
2FYGA native 128 Decoy_pdb (5000) Decoy_spicker Best_decoy (11.46/0.263) Closc.pdb (14.56/0.251)
2OQ8A native 150 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.56/0.313) Closc.pdb (13.74/0.276)
1KVDB native 77 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.41/0.376) Closc.pdb (10.65/0.250)
1KP6A native 79 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.46/0.344) Closc.pdb (  9.68/0.330)
1R77B native 103 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.98/0.335) Closc.pdb (11.75/0.313)
2J97A native 98 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.08/0.304) Closc.pdb (14.99/0.241)
1KPTA native 105 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.80/0.325) Closc.pdb (13.01/0.261)
1TSFA native 81 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.50/0.362) Closc.pdb (13.50/0.292)
2E12A native 93 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.25/0.395) Closc.pdb (14.42/0.256)
2F5GA native 130 Decoy_pdb (5000) Decoy_spicker Best_decoy (11.25/0.361) Closc.pdb (18.02/0.284)
2HL7A native 82 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.46/0.648) Closc.pdb (  7.95/0.421)
1T1JB native 125 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.88/0.297) Closc.pdb (15.63/0.281)
2OQBB native 106 Decoy_pdb (5000) Decoy_spicker Best_decoy (11.28/0.314) Closc.pdb (14.54/0.259)
1YO3A native 85 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.72/0.546) Closc.pdb (11.04/0.316)
1DJ7A native 109 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.82/0.429) Closc.pdb (11.93/0.315)
1VCCA native 77 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.73/0.576) Closc.pdb (  5.72/0.386)
2D68B native 77 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.38/0.469) Closc.pdb (10.76/0.411)
1ZKEA native 81 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.17/0.528) Closc.pdb (  8.32/0.380)
2CIUA native 123 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.68/0.628) Closc.pdb (15.55/0.425)
3BS1A native 103 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.72/0.446) Closc.pdb (12.89/0.234)
1G8QA native 90 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.88/0.352) Closc.pdb (  9.04/0.473)
1RKIA native 101 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.46/0.338) Closc.pdb (  9.81/0.235)
2AYDA native 76 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.60/0.325) Closc.pdb (10.12/0.303)
1T92A native 108 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.93/0.418) Closc.pdb (10.05/0.465)
2Q3TA native 121 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.91/0.323) Closc.pdb (16.25/0.217)
2CZSA native 70 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.26/0.505) Closc.pdb (  7.61/0.351)
1JR8A native 105 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.52/0.506) Closc.pdb (11.65/0.314)
1LMIA native 131 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.90/0.356) Closc.pdb (16.73/0.219)
1DP7P native 76 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.27/0.558) Closc.pdb (13.00/0.407)
1VYIA native 111 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.25/0.404) Closc.pdb (13.38/0.291)
1WPUA native 147 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.24/0.397) Closc.pdb (16.00/0.322)
1XAWA native 107 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.31/0.795) Closc.pdb (21.98/0.404)
1BGFA native 124 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.10/0.358) Closc.pdb (15.25/0.269)
2HEWF native 128 Decoy_pdb (5000) Decoy_spicker Best_decoy (12.61/0.297) Closc.pdb (16.43/0.213)
2OHWA native 128 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.11/0.421) Closc.pdb (11.46/0.363)
1N13B native 112 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.34/0.455) Closc.pdb (  9.68/0.359)
1MC2A native 122 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.25/0.538) Closc.pdb (11.20/0.326)
2B97A native 70 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.49/0.353) Closc.pdb (  9.83/0.306)
2VB1A native 129 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.81/0.292) Closc.pdb (12.85/0.284)
1JO0A native 97 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.17/0.672) Closc.pdb (11.23/0.356)
1WCKA native 136 Decoy_pdb (5000) Decoy_spicker Best_decoy (12.83/0.243) Closc.pdb (16.60/0.181)
1IJYA native 122 Decoy_pdb (5000) Decoy_spicker Best_decoy (  6.82/0.477) Closc.pdb (12.70/0.273)
1VMHA native 129 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.93/0.347) Closc.pdb (15.58/0.208)
2QT7A native 89 Decoy_pdb (5000) Decoy_spicker Best_decoy (  3.30/0.626) Closc.pdb (  6.14/0.460)
2J6BA native 109 Decoy_pdb (5000) Decoy_spicker Best_decoy (10.70/0.310) Closc.pdb (13.79/0.273)
2QSBA native 82 Decoy_pdb (5000) Decoy_spicker Best_decoy (  2.52/0.696) Closc.pdb (  3.25/0.601)
1NQJB native 114 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.43/0.295) Closc.pdb (11.88/0.271)
2BT9A native 90 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.98/0.399) Closc.pdb (10.02/0.308)
2H8EA native 120 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.70/0.325) Closc.pdb (17.45/0.285)
1VR7A native 119 Decoy_pdb (5000) Decoy_spicker Best_decoy (  8.58/0.368) Closc.pdb (11.50/0.314)
1SAUA native 114 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.65/0.536) Closc.pdb (11.64/0.312)
1UZ3A native 102 Decoy_pdb (5000) Decoy_spicker Best_decoy (  9.50/0.456) Closc.pdb (15.16/0.375)
2AXWA native 134 Decoy_pdb (5000) Decoy_spicker Best_decoy (15.83/0.232) Closc.pdb (19.23/0.243)
1LWBA native 122 Decoy_pdb (5000) Decoy_spicker Best_decoy (  5.47/0.502) Closc.pdb (12.03/0.293)
1I27A native 73 Decoy_pdb (5000) Decoy_spicker Best_decoy (  4.91/0.453) Closc.pdb (  7.46/0.569)
2AIBA native 98 Decoy_pdb (5000) Decoy_spicker Best_decoy (  7.48/0.413) Closc.pdb (10.34/0.286)
1C5EA native 95 Decoy_pdb (5000) Decoy_spicker Best_decoy (11.09/0.223) Closc.pdb (12.89/0.188)
Average 107 (  7.30/0.446) (11.75/0.341)



References:
D. Xu, Y. Zhang, Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins, 2012, 80, 1715-1735 (download the PDF file and Support Information).

yangzhanglabumich.edu | (734) 647-1549 | 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218