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)).

  • 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)



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).
 


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