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I-TASSER Decoy Set-II

This page contains the atomic structure decoys of 56 non-homologous small proteins (Decoy Set II), which is a non-rudundant subset of the I-TASSER decoys (Set-I). The raw decoys were first generated by I-TASSER ab initio simulation, which were then structurally refined by GROMACS4.0 using OPLS-AA force field with the purpose of removing steric clashes and refining torsion angles. Each set includes 300-500 decoys, which was used to test the atomic potentials, including RW and RWplus potentials (see, J Zhang and Y Zhang, A Distance-Dependent Atomic Potential Derived from Random-Walk Ideal Chain Reference State for Protein Fold Selection and Structure Prediction. PLoS One, vol 5, e15386 (2010)).

• The whole set I-TASSER decoys without MD refinement (Decoy Set-I) are available at http://zhanglab.dcmb.med.umich.edu/decoys/decoy1.html.

• To download the decoys for all 56 proteins: All decoys

Explanations:

• ID---------------PDB ID of the target proteins.
• Native-----------Experimental structure from the PDB library.
• Length-----------Size of the target proteins.
• DecoyAll---------The tar file of all structure decoys in standard PDB format; numbers in parathesis are number of decoys.
• DecoySpk---------The same as 'DecoyAll', but converted to the format that can be directly used by SPICKER.
• BestDecoy--------The best decoy with the lowest RMSD to the native; 'R/TM' are RMSD/TM-score to the native structure.
• Decoy_Spk--------The first model selected by SPICKER, which is the decoy closest to the first SPICKER cluster centroid.
• Deocy_RW---------The first selected model with the lowest RW potential.
• Plot-------------The plot of C-alpha RMSD to native structure vs RW potential.

ID	Native	Length	DecoyAll (#)	DecoySpk	BestDecoy (R/TM)	Decoy_Spk (R/TM)	Decoy_RW (R/TM)	RW_energy vs RMSD
1abv_	native	103	DecoyAll (526)	DecoySpk	Best (4.90/0.507)	Closc (8.22/0.381)	modRW (13.61/0.276)
1af7__	native	72	DecoyAll (527)	DecoySpk	Best (3.04/0.623)	Closc (4.18/0.487)	modRW (4.49/0.452)
1ah9_	native	63	DecoyAll (510)	DecoySpk	Best (2.22/0.696)	Closc (6.26/0.466)	modRW (2.22/0.696)
1aoy_	native	65	DecoyAll (529)	DecoySpk	Best (2.69/0.711)	Closc (4.23/0.669)	modRW (4.19/0.644)
1b4bA	native	71	DecoyAll (460)	DecoySpk	Best (4.23/0.473)	Closc (8.98/0.450)	modRW (5.87/0.450)
1b72A	native	49	DecoyAll (534)	DecoySpk	Best (2.50/0.697)	Closc (4.38/0.492)	modRW (2.99/0.642)
1bm8_	native	99	DecoyAll (329)	DecoySpk	Best (6.70/0.388)	Closc (6.86/0.355)	modRW (11.83/0.342)
1bq9A	native	53	DecoyAll (573)	DecoySpk	Best (3.96/0.465)	Closc (7.85/0.387)	modRW (7.03/0.397)
1cewI	native	108	DecoyAll (452)	DecoySpk	Best (3.25/0.748)	Closc (3.86/0.719)	modRW (4.02/0.705)
1cqkA	native	101	DecoyAll (284)	DecoySpk	Best (1.45/0.885)	Closc (1.68/0.854)	modRW (1.71/0.871)
1csp_	native	67	DecoyAll (315)	DecoySpk	Best (2.04/0.753)	Closc (2.44/0.716)	modRW (2.44/0.711)
1cy5A	native	92	DecoyAll (273)	DecoySpk	Best (1.30/0.893)	Closc (1.40/0.884)	modRW (1.65/0.857)
1dcjA_	native	73	DecoyAll (525)	DecoySpk	Best (9.42/0.368)	Closc (12.67/0.326)	modRW (11.00/0.347)
1di2A_	native	69	DecoyAll (374)	DecoySpk	Best (1.49/0.843)	Closc (2.20/0.766)	modRW (3.04/0.758)
1dtjA_	native	74	DecoyAll (285)	DecoySpk	Best (1.77/0.814)	Closc (2.15/0.790)	modRW (5.65/0.709)
1egxA	native	115	DecoyAll (352)	DecoySpk	Best (2.08/0.827)	Closc (2.59/0.767)	modRW (2.73/0.779)
1fadA	native	92	DecoyAll (514)	DecoySpk	Best (2.95/0.652)	Closc (3.62/0.576)	modRW (3.76/0.576)
1fo5A	native	85	DecoyAll (340)	DecoySpk	Best (3.63/0.568)	Closc (3.83/0.530)	modRW (4.13/0.497)
1g1cA	native	98	DecoyAll (307)	DecoySpk	Best (2.26/0.787)	Closc (2.67/0.773)	modRW (2.61/0.770)
1gjxA	native	77	DecoyAll (525)	DecoySpk	Best (5.22/0.515)	Closc (7.12/0.430)	modRW (11.41/0.224)
1gnuA	native	117	DecoyAll (553)	DecoySpk	Best (4.12/0.647)	Closc (10.56/0.546)	modRW (8.26/0.573)
1gpt_	native	47	DecoyAll (469)	DecoySpk	Best (3.20/0.553)	Closc (5.14/0.493)	modRW (7.76/0.510)
1gyvA	native	117	DecoyAll (337)	DecoySpk	Best (3.03/0.776)	Closc (3.46/0.741)	modRW (3.91/0.742)
1hbkA	native	89	DecoyAll (300)	DecoySpk	Best (2.83/0.708)	Closc (3.46/0.663)	modRW (13.10/0.291)
1itpA	native	68	DecoyAll (526)	DecoySpk	Best (4.43/0.511)	Closc (8.07/0.310)	modRW (11.22/0.324)
1jnuA	native	104	DecoyAll (269)	DecoySpk	Best (2.48/0.768)	Closc (2.95/0.724)	modRW (3.09/0.722)
1kjs_	native	74	DecoyAll (548)	DecoySpk	Best (4.68/0.500)	Closc (8.45/0.373)	modRW (8.47/0.374)
1kviA	native	68	DecoyAll (550)	DecoySpk	Best (1.65/0.790)	Closc (2.29/0.677)	modRW (2.29/0.677)
1mkyA3	native	81	DecoyAll (285)	DecoySpk	Best (3.78/0.552)	Closc (5.50/0.415)	modRW (6.09/0.353)
1mla_2	native	70	DecoyAll (335)	DecoySpk	Best (2.36/0.775)	Closc (3.23/0.623)	modRW (4.00/0.529)
1mn8A	native	84	DecoyAll (545)	DecoySpk	Best (5.32/0.457)	Closc (6.81/0.329)	modRW (13.86/0.270)
1n0uA4	native	69	DecoyAll (301)	DecoySpk	Best (3.42/0.588)	Closc (4.93/0.452)	modRW (3.72/0.528)
1ne3A	native	56	DecoyAll (566)	DecoySpk	Best (3.49/0.453)	Closc (6.52/0.372)	modRW (5.45/0.411)
1no5A	native	93	DecoyAll (426)	DecoySpk	Best (6.26/0.419)	Closc (10.94/0.405)	modRW (10.58/0.404)
1npsA	native	88	DecoyAll (469)	DecoySpk	Best (1.97/0.800)	Closc (2.21/0.767)	modRW (2.47/0.752)
1o2fB_	native	77	DecoyAll (510)	DecoySpk	Best (4.17/0.528)	Closc (11.02/0.269)	modRW (5.92/0.427)
1of9A	native	77	DecoyAll (507)	DecoySpk	Best (3.16/0.585)	Closc (3.94/0.494)	modRW (3.69/0.518)
1ogwA_	native	72	DecoyAll (520)	DecoySpk	Best (1.12/0.890)	Closc (1.31/0.862)	modRW (1.66/0.799)
1orgA	native	118	DecoyAll (442)	DecoySpk	Best (2.18/0.816)	Closc (2.75/0.744)	modRW (2.86/0.724)
1pgx_	native	59	DecoyAll (562)	DecoySpk	Best (2.80/0.551)	Closc (5.80/0.445)	modRW (3.67/0.479)
1r69_	native	61	DecoyAll (291)	DecoySpk	Best (1.39/0.824)	Closc (2.07/0.726)	modRW (1.79/0.749)
1sfp_	native	111	DecoyAll (308)	DecoySpk	Best (4.82/0.758)	Closc (5.31/0.745)	modRW (5.52/0.738)
1shfA	native	59	DecoyAll (536)	DecoySpk	Best (1.42/0.836)	Closc (3.34/0.507)	modRW (1.98/0.738)
1sro_	native	71	DecoyAll (515)	DecoySpk	Best (2.60/0.648)	Closc (3.86/0.616)	modRW (3.46/0.624)
1ten_	native	87	DecoyAll (294)	DecoySpk	Best (1.55/0.851)	Closc (1.85/0.822)	modRW (2.20/0.761)
1tfi_	native	47	DecoyAll (339)	DecoySpk	Best (2.46/0.592)	Closc (4.69/0.558)	modRW (4.30/0.433)
1thx_	native	108	DecoyAll (302)	DecoySpk	Best (1.72/0.865)	Closc (2.26/0.800)	modRW (2.18/0.805)
1tif_	native	59	DecoyAll (542)	DecoySpk	Best (6.57/0.340)	Closc (7.75/0.320)	modRW (9.20/0.288)
1tig_	native	88	DecoyAll (565)	DecoySpk	Best (3.38/0.585)	Closc (9.45/0.418)	modRW (4.51/0.542)
1vcc_	native	76	DecoyAll (551)	DecoySpk	Best (4.84/0.455)	Closc (6.54/0.407)	modRW (6.81/0.388)
256bA	native	106	DecoyAll (506)	DecoySpk	Best (2.74/0.814)	Closc (3.72/0.758)	modRW (3.83/0.724)
2a0b_	native	118	DecoyAll (282)	DecoySpk	Best (2.19/0.838)	Closc (2.42/0.808)	modRW (2.42/0.802)
2cr7A	native	60	DecoyAll (540)	DecoySpk	Best (2.56/0.666)	Closc (3.49/0.514)	modRW (4.19/0.445)
2f3nA	native	65	DecoyAll (485)	DecoySpk	Best (1.65/0.758)	Closc (2.35/0.713)	modRW (2.79/0.604)
2pcy_	native	99	DecoyAll (435)	DecoySpk	Best (3.91/0.637)	Closc (4.56/0.623)	modRW (4.61/0.632)
2reb_2	native	60	DecoyAll (550)	DecoySpk	Best (4.38/0.403)	Closc (7.07/0.317)	modRW (6.89/0.488)
Average		80			(3.245/0.6563)	(4.951/0.5745)	(5.270/0.5691)

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References:
J Zhang and Y Zhang, A Distance-Dependent Atomic Potential Derived from Random-Walk Ideal Chain Reference State for Protein Fold Selection and Structure Prediction. PLoS One, vol 5, e15386 (2010). (download PDF file).