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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--------------------PDB ID of the target proteins.
• Native--------------Experimental structure from the PDB library.
• Length-------------Size of the target proteins.
• Decoy_pdb-------The full-atomic QUARK decoys in standard PDB format; numbers in parathesis are the number of decoys.
• Decoy_Spicker--Same as 'Decoys_pdb', but it is Ca-only traces and converted to the format that can be directly used by SPICKER.
• Best_decoy------The best decoy with the lowest RMSD to the native; 'RMSD/TM' are RMSD/TM-score to the native structure.
• Closc--------------The first model selected by SPICKER, which is the decoy closest to the first SPICKER cluster centroid.

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)

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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).