TABLE 6.
Summary of fold results on 125 benchmark proteins
| ID* | Str† | N‡ | Clusterwo§ | Clusterw¶ | Comb‖ | E1** | M1†† | Y1‡‡ | D1§§ | Bests¶¶ |
|---|---|---|---|---|---|---|---|---|---|---|
| Set65‖‖ | ||||||||||
| 1a32_ | α | 64 | 4.63(3/3) | 6.30(1/3) | 6.30 | 6.30★ | 6.30★ | 6.30★ | 6.30★ | 4.57(435) |
| 1ah9_ | β | 63 | 6.20(1/11) | 5.09(1/5) | 5.09 | 5.09★ | 5.09★ | 5.09★ | 5.09★ | 3.18(324) |
| 1aoy_⋆ | α | 65 | 6.84(4/5) | 4.68(1/9) | 4.68 | 4.68★ | 4.68★ | 4.68★ | 4.68★ | 2.22(325) |
| 1bq9A | β | 53 | 7.05(7/19) | 4.82(1/13) | 4.82 | 4.82★ | 4.82★ | 4.82★ | 4.82★ | 2.87(123) |
| 1bw6A | α | 56 | 4.79(2/3) | 4.22(1/8) | 4.22 | 4.22★ | 4.22★ | 4.22★ | 4.22★ | 2.96(699) |
| 1c5a_⋆ | α | 65 | 4.28(2/7) | 4.25(2/4) | 4.25 | 8.25 | 8.25 | 8.25 | 8.25 | 3.16(554) |
| 1cewI | αβ | 108 | 10.96(1/14) | 6.33(2/7) | 6.33 | 9.02 | 9.02 | 9.02 | 9.02 | 3.82(763) |
| 1cis_⋆ | αβ | 66 | 5.12(4/9) | 5.92(3/3) | 5.92 | 6.65 | 6.65 | 6.65 | 6.65 | 3.96(493) |
| 1csp_ | β | 67 | 6.37(4/11) | 3.84(2/5) | 3.84 | 10.57 | 4.32 | 4.32 | 4.32 | 3.36(211) |
| 1ctf_⋆ | αβ | 68 | 5.54(3/4) | 5.24(2/11) | 5.24 | 9.91 | 9.91 | 9.91 | 9.91 | 3.94(777) |
| 1erv_⋆ | αβ | 105 | 6.01(3/6) | 2.09(1/8) | 2.09 | 2.09★ | 2.09★ | 2.09★ | 2.09★ | 1.86(187) |
| 1fas_⋆ | β | 61 | 6.81(5/29) | 3.21(1/4) | 3.21 | 3.21★ | 3.21★ | 3.21★ | 3.21★ | 2.42(676) |
| 1fc2C | α | 43 | 3.61(1/4) | 3.92(1/4) | 3.61 | 3.92★ | 3.92★ | 3.92★ | 3.92★ | 2.58(93) |
| 1ftz_⋆ | α | 48 | 5.07(1/2) | 1.66(1/7) | 1.66 | 1.66★ | 1.66★ | 1.66★ | 1.66★ | 1.20(311) |
| 1gpt_⋆ | αβ | 47 | 6.30(1/25) | 3.96(1/10) | 3.96 | 3.96★ | 3.96★ | 3.96★ | 3.96★ | 2.19(214) |
| 1hlb_ | α | 157 | 7.02(8/11) | 4.68(1/10) | 4.68 | 4.68★ | 4.68★ | 4.68★ | 4.68★ | 3.36(65) |
| 1hmdA⋆ | α | 113 | 7.58(1/6) | 9.12(5/9) | 7.58 | 13.99 | 9.12★ | 9.12★ | 9.12★ | 6.59(270) |
| 1hp8_ | α | 68 | 4.67(2/3) | 5.26(1/4) | 5.26 | 5.26★ | 5.26★ | 5.26★ | 5.26★ | 4.14(319) |
| 1ife_ | αβ | 91 | 4.60(1/5) | 8.76(4/4) | 4.60 | 11.68 | 11.68 | 11.68 | 11.68 | 3.93(427) |
| 1ixa_ | β | 39 | 6.04(4/31) | 4.30(1/5) | 4.30 | 4.30★ | 4.30★ | 4.30★ | 4.30★ | 2.40(648) |
| 1iyv_ | β | 74 | 8.43(1/15) | 7.60(2/9) | 7.60 | 9.69 | 7.60★ | 7.60★ | 7.60★ | 6.28(407) |
| 1kjs_⋆ | α | 74 | 5.54(1/4) | 8.23(2/3) | 5.54 | 10.03 | 10.03 | 10.03 | 10.03 | 5.34(119) |
| 1ksr_⋆ | β | 100 | 8.03(5/16) | 5.82(1/8) | 5.82 | 5.82★ | 5.82★ | 5.82★ | 5.82★ | 4.57(133) |
| 1lea_⋆ | α | 72 | 5.69(5/5) | 4.22(1/8) | 4.22 | 4.22★ | 4.22★ | 4.22★ | 4.22★ | 2.92(79) |
| 1mba_⋆ | α | 146 | 10.25(3/11) | 2.51(1/6) | 2.51 | 2.51★ | 2.51★ | 2.51★ | 2.51★ | 2.10(804) |
| 1ner_ | α | 64 | 6.35(2/8) | 2.70(1/11) | 2.70 | 2.70★ | 2.70★ | 2.70★ | 2.70★ | 2.28(174) |
| 1ngr_ | α | 83 | 5.19(5/6) | 3.39(1/7) | 3.39 | 3.39★ | 4.80 | 3.39★ | 4.80 | 2.57(524) |
| 1nkl_ | α | 77 | 5.50(2/7) | 3.89(1/6) | 3.89 | 3.89★ | 3.89★ | 3.89★ | 3.89★ | 2.91(356) |
| 1nxb_⋆ | β | 62 | 6.08(3/19) | 2.35(1/7) | 2.35 | 2.35★ | 2.35★ | 2.35★ | 2.35★ | 2.13(393) |
| 1pdo_⋆ | αβ | 124 | 6.98(2/15) | 6.66(1/3) | 6.66 | 6.66★ | 8.56 | 6.66★ | 6.66★ | 5.34(102) |
| 1pgx_ | αβ | 59 | 5.62(3/7) | 5.96(5/7) | 9.30 | 10.80 | 9.31 | 9.31 | 5.96★ | 4.22(24) |
| 1poh_ | αβ | 85 | 9.10(5/9) | 12.71(4/6) | 12.71 | 12.74 | 12.74 | 12.74 | 12.74 | 9.93(10) |
| 1pou_ | α | 69 | 4.41(5/9) | 4.22(4/7) | 4.22 | 9.57 | 9.57 | 9.57 | 9.57 | 3.38(47) |
| 1pse_⋆ | β | 68 | 9.55(2/13) | 7.88(9/11) | 9.15 | 10.81 | 10.81 | 10.81 | 10.81 | 5.81(682) |
| 1rip_ | β | 76 | 7.97(5/8) | 8.53(2/7) | 8.53 | 9.41 | 9.41 | 9.41 | 9.41 | 7.21(236) |
| 1rpo_ | α | 61 | 5.47(1/3) | 4.55(1/2) | 4.55 | 4.55★ | 24.82 | 4.55★ | 4.55★ | 3.18(456) |
| 1shaA⋆ | αβ | 103 | 8.66(7/13) | 4.05(1/10) | 4.05 | 4.05★ | 4.05★ | 4.05★ | 4.05★ | 2.95(595) |
| 1shg_ | β | 57 | 7.62(7/8) | 4.59(2/8) | 4.59 | 9.89 | 10.40 | 10.40 | 10.40 | 3.54(499) |
| 1sro_⋆ | β | 71 | 7.65(1/7) | 4.27(1/8) | 4.27 | 4.27★ | 4.27★ | 4.27★ | 4.27★ | 3.21(107) |
| 1stfI | αβ | 98 | 8.79(1/12) | 4.92(1/9) | 4.92 | 4.92★ | 4.92★ | 4.92★ | 4.92★ | 2.91(551) |
| 1stu_⋆ | αβ | 68 | 7.68(2/6) | 6.31(2/6) | 6.31 | 6.72 | 6.72 | 6.72 | 6.72 | 4.97(101) |
| 1tfi_⋆ | β | 47 | 6.79(2/2) | 6.22(2/7) | 6.22 | 10.23 | 6.22★ | 6.22★ | 6.22★ | 4.35(526) |
| 1thx_ | β | 108 | 6.22(3/10) | 2.33(1/6) | 2.33 | 2.33★ | 2.33★ | 2.33★ | 2.33★ | 2.10(547) |
| 1tit_ | β | 89 | 7.88(7/15) | 1.88(1/10) | 1.88 | 1.88★ | 5.45 | 1.88★ | 1.88★ | 1.71(896) |
| 1tlk_ | β | 95 | 9.27(4/21) | 2.24(1/6) | 2.24 | 2.24★ | 2.24★ | 2.24★ | 2.24★ | 1.99(868) |
| 1tsg_ | αβ | 98 | 8.19(15/18) | 9.08(3/9) | 9.08 | 12.49 | 9.08★ | 9.08★ | 9.08★ | 6.64(840) |
| 1ubi_⋆ | αβ | 72 | 6.60(3/7) | 1.74(1/11) | 1.74 | 1.74★ | 1.74★ | 1.74★ | 1.74★ | 1.54(821) |
| 1vcc_ | αβ | 76 | 7.07(3/16) | 7.29(12/15) | 7.42 | 7.42 | 10.70 | 10.70 | 10.70 | 6.54(68) |
| 1vif_ | β | 52 | 6.87(9/12) | 7.93(3/9) | 7.12 | 8.58 | 7.93★ | 7.93★ | 7.93★ | 5.33(215) |
| 1wiu_ | β | 93 | 9.95(2/10) | 2.22(1/8) | 2.22 | 2.22★ | 2.22★ | 2.22★ | 2.22★ | 1.96(619) |
| 256bA⋆ | α | 106 | 3.61(2/3) | 3.18(2/7) | 3.18 | 8.60 | 3.19★ | 3.19★ | 3.19★ | 2.17(685) |
| 2af8_⋆ | α | 86 | 11.07(5/6) | 3.68(1/9) | 3.68 | 3.69★ | 6.87 | 3.69★ | 3.69★ | 3.19(463) |
| 2azaA⋆ | β | 129 | 10.20(38/51) | 2.79(1/13) | 2.79 | 2.79★ | 2.79★ | 2.79★ | 2.79★ | 2.66(475) |
| 2bby_⋆ | α | 67 | 9.10(4/6) | 6.65(2/6) | 6.65 | 9.71 | 9.71 | 9.71 | 9.71 | 4.34(35) |
| 2ezh_⋆ | α | 65 | 5.78(3/3) | 4.74(3/5) | 4.74 | 8.69 | 4.74★ | 4.74★ | 4.74★ | 3.13(377) |
| 2ezk_⋆ | α | 90 | 8.06(4/7) | 8.98(4/6) | 8.98 | 12.59 | 12.39 | 12.39 | 12.39 | 7.28(278) |
| 2fdn_⋆ | αβ | 55 | 5.73(1/41) | 2.27(1/12) | 2.27 | 2.27★ | 2.27★ | 2.27★ | 2.27★ | 1.97(542) |
| 2fmr_ | αβ | 64 | 5.66(5/9) | 4.97(1/9) | 4.97 | 4.96★ | 4.96★ | 4.96★ | 4.96★ | 3.98(216) |
| 2lfb_ | α | 70 | 7.47(2/5) | 6.37(4/7) | 6.37 | 10.29 | 10.29 | 10.29 | 10.29 | 5.95(35) |
| 2pcy_ | β | 99 | 8.00(4/36) | 4.25(1/11) | 4.25 | 4.25★ | 4.25★ | 4.25★ | 4.25★ | 3.47(135) |
| 2ptl_⋆ | αβ | 61 | 3.32(1/5) | 2.63(1/6) | 2.63 | 2.63★ | 2.63★ | 2.63★ | 2.63★ | 2.02(528) |
| 2sarA⋆ | αβ | 96 | 9.57(11/36) | 7.55(4/7) | 7.55 | 11.36 | 11.36 | 11.36 | 11.36 | 5.35(666) |
| 4fgf_ | β | 124 | 10.40(29/49) | 3.75(2/13) | 3.75 | 6.11 | 3.75★ | 6.11 | 3.75★ | 3.11(492) |
| 5fd1_ | αβ | 106 | 9.19(3/8) | 5.79(1/6) | 5.79 | 5.79★ | 10.69 | 5.79★ | 5.79★ | 4.76(303) |
| 6pti_ | αβ | 56 | 5.02(2/8) | 4.04(5/9) | 6.31 | 6.31 | 4.04★ | 4.04★ | 4.04★ | 3.48(545) |
| Set60*** | ||||||||||
| 1ail_ | α | 70 | 7.31(1/3) | 4.01(2/5) | 4.01 | 8.44 | 8.44 | 8.44 | 8.44 | 2.77(565) |
| 1aiw_ | β | 62 | 8.75(4/34) | 8.07(4/19) | 8.07 | 8.74 | 9.76 | 8.74 | 9.76 | 6.95(269) |
| 1amm_ | αβ | 174 | 12.86(62/62) | 10.08(1/6) | 10.08 | 10.08★ | 13.84 | 13.84 | 13.84 | 9.06(998) |
| 1apf_ | β | 49 | 6.04(5/27) | 4.43(2/10) | 4.43 | 9.31 | 6.59 | 9.31 | 9.31 | 4.31(228) |
| 1b2pA | β | 119 | 12.52(31/56) | 11.39(19/32) | 12.09 | 13.93 | 12.31 | 12.60 | 12.31 | 10.53(613) |
| 1bd8_ | α | 156 | 13.36(3/8) | 3.03(1/11) | 3.03 | 3.03★ | 3.03★ | 3.03★ | 3.03★ | 2.22(629) |
| 1bfg_ | β | 126 | 10.71(32/54) | 3.72(1/13) | 3.72 | 3.72★ | 3.72★ | 3.72★ | 3.72★ | 3.20(831) |
| 1bkf_ | αβ | 107 | 8.49(5/24) | 7.52(3/16) | 7.52 | 14.21 | 12.45 | 12.45 | 12.45 | 6.65(973) |
| 1bkrA | α | 108 | 7.82(3/7) | 2.12(1/14) | 2.12 | 2.12★ | 2.12★ | 2.12★ | 2.12★ | 1.76(785) |
| 1bm8_ | αβ | 99 | 8.11(8/19) | 8.98(2/11) | 8.98 | 11.91 | 9.84 | 9.84 | 9.84 | 8.53(399) |
| 1c3mA | β | 145 | 11.02(27/36) | 10.53(5/20) | 12.96 | 14.98 | 10.53★ | 12.96 | 10.53★ | 9.55(551) |
| 1c8cA | αβ | 64 | 8.97(26) | 8.72(5/7) | 10.24 | 10.24 | 11.87 | 11.87 | 11.87 | 8.41(4) |
| 1cpq_ | α | 129 | 9.76(3/7) | 6.26(5/5) | 10.90 | 15.43 | 10.90 | 10.90 | 6.26★ | 5.16(498) |
| 1cy5A | α | 92 | 11.60(3/5) | 1.76(1/9) | 1.76 | 1.76★ | 1.76★ | 1.76★ | 1.76★ | 1.47(711) |
| 1dhn_ | αβ | 121 | 9.47(1/14) | 2.91(1/11) | 2.91 | 2.91★ | 2.91★ | 2.91★ | 2.91★ | 2.41(554) |
| 1dxgA | β | 36 | 6.46(3/11) | 4.46(3/7) | 4.46 | 7.44 | 6.15 | 6.15 | 6.15 | 3.46(143) |
| 1e6iA | α | 110 | 8.42(4/7) | 12.07(2/3) | 12.00 | 22.98 | 12.07★ | 12.07★ | 12.07★ | 10.28(2) |
| 1eca_ | α | 136 | 10.12(3/10) | 3.37(1/10) | 3.37 | 3.37★ | 3.37★ | 3.37★ | 3.37★ | 2.67(862) |
| 1eq7A | α | 56 | 7.01(3/3) | 3.72(2/5) | 3.72 | 17.15 | 17.15 | 17.15 | 17.15 | 1.89(84) |
| 1ezgA | β | 82 | 11.03(40/44) | 9.38(4/9) | 9.38 | 11.22 | 9.38★ | 9.38★ | 9.38★ | 9.13(24) |
| 1f4pA | αβ | 147 | 7.83(2/13) | 2.80(1/14) | 2.80 | 2.80★ | 2.80★ | 2.80★ | 2.80★ | 2.64(880) |
| 1f94A | β | 63 | 8.22(13/24) | 3.92(1/12) | 3.92 | 3.92★ | 3.92★ | 3.92★ | 3.92★ | 3.56(601) |
| 1fazA | α | 122 | 9.01(3/11) | 10.84(3/12) | 10.84 | 12.82 | 12.24 | 12.24 | 12.24 | 8.59(477) |
| 1fk5A | α | 93 | 4.10(2/9) | 5.05(2/5) | 5.05 | 9.21 | 5.05★ | 5.05★ | 5.05★ | 4.07(421) |
| 1fna_ | β | 91 | 5.11(1/9) | 3.06(1/11) | 3.06 | 3.06★ | 3.06★ | 3.06★ | 3.06★ | 2.74(367) |
| 1fw9A | αβ | 164 | 14.11(13/20) | 13.71(5/22) | 14.26 | 14.26 | 13.77 | 13.77 | 13.77 | 12.78(866) |
| 1gnuA | αβ | 117 | 10.79(3/12) | 9.34(11/13) | 11.76 | 14.72 | 14.72 | 14.72 | 14.72 | 9.07(56) |
| 1hbkA | α | 89 | 8.19(4/9) | 8.52(2/7) | 8.52 | 14.54 | 14.84 | 14.54 | 14.84 | 7.45(329) |
| 1hoe_ | β | 74 | 9.39(5/13) | 8.57(1/12) | 8.57 | 8.57★ | 10.19 | 10.19 | 10.19 | 6.91(216) |
| 1i27A | αβ | 73 | 9.11(3/6) | 5.60(2/7) | 5.60 | 7.79 | 7.79 | 7.79 | 7.79 | 4.45(305) |
| 1i2tA | α | 61 | 3.64(1/6) | 2.49(2/6) | 2.49 | 10.20 | 10.20 | 2.49★ | 2.49★ | 1.80(151) |
| 1isuA | α | 62 | 5.54(6/22) | 2.65(1/14) | 2.65 | 2.65★ | 2.65★ | 2.65★ | 2.65★ | 2.02(538) |
| 1koe_ | αβ | 172 | 13.02(22/50) | 14.45(5/8) | 15.22 | 16.18 | 16.35 | 16.35 | 16.35 | 13.67(15) |
| 1kp6A | αβ | 79 | 10.01(8/14) | 9.69(2/15) | 9.69 | 9.73 | 9.73 | 9.73 | 9.73 | 8.10(909) |
| 1lid_ | αβ | 131 | 11.42(2/47) | 2.32(1/13) | 2.32 | 2.32★ | 2.32★ | 2.32★ | 2.32★ | 2.22(530) |
| 1lkkA | αβ | 105 | 7.57(9/20) | 3.87(1/11) | 3.87 | 3.87★ | 3.87★ | 3.87★ | 3.87★ | 2.85(854) |
| 1msi_ | β | 66 | 7.72(19/28) | 4.40(5/26) | 9.22 | 10.94 | 8.85 | 10.25 | 4.40★ | 3.96(947) |
| 1nbcA | αβ | 155 | 12.60(14/45) | 5.77(1/13) | 5.77 | 5.77★ | 5.77★ | 5.77★ | 5.77★ | 4.97(903) |
| 1nkd_ | α | 59 | 1.78(1/2) | 4.21(2/2) | 1.78 | 23.81 | 23.81 | 23.81 | 23.81 | 3.15(212) |
| 1npsA | αβ | 88 | 6.89(33/34) | 3.42(1/13) | 3.42 | 3.42★ | 3.42★ | 3.42★ | 3.42★ | 3.09(880) |
| 1opd_ | αβ | 85 | 3.55(1/9) | 10.21(4/8) | 3.55 | 13.24 | 13.24 | 13.24 | 13.24 | 8.81(9) |
| 1ppt_ | α | 36 | 1.92(1/2) | 7.00(3/5) | 1.92 | 7.64 | 7.64 | 7.64 | 7.64 | 3.25(7) |
| 1qj8A | β | 148 | 12.00(8/43) | 12.13(2/10) | 12.13 | 17.99 | 12.13★ | 12.13★ | 12.13★ | 11.00(1) |
| 1qqhA | αβ | 144 | 13.58(8/30) | 14.46(15/16) | 16.68 | 17.08 | 16.68 | 17.08 | 16.68 | 13.02(9) |
| 1qstA | αβ | 160 | 9.09(6/20) | 7.50(1/3) | 7.50 | 7.50★ | 7.50★ | 7.50★ | 7.50★ | 5.38(497) |
| 1sfp_ | β | 111 | 7.48(2/18) | 6.00(1/13) | 6.00 | 6.00★ | 13.26 | 6.00★ | 13.26 | 5.75(625) |
| 1sra_ | α | 151 | 10.71(3/12) | 11.09(1/10) | 11.09 | 11.09★ | 11.09★ | 11.09★ | 11.09★ | 8.64(144) |
| 1t1dA | αβ | 100 | 8.96(7/13) | 3.63(1/13) | 3.63 | 3.63★ | 3.63★ | 3.63★ | 3.63★ | 2.72(357) |
| 1tul_ | β | 102 | 6.87(6/19) | 8.13(3/12) | 8.13 | 10.41 | 9.49 | 9.49 | 9.49 | 6.11(977) |
| 1utg_ | α | 70 | 6.24(3/5) | 4.93(3/5) | 4.93 | 12.87 | 12.87 | 12.87 | 12.87 | 4.26(138) |
| 1who_ | β | 94 | 5.24(4/24) | 5.29(1/12) | 5.29 | 5.29★ | 5.29★ | 5.29★ | 5.29★ | 3.10(887) |
| 1wkt_ | β | 88 | 6.75(14/47) | 10.92(4/23) | 10.92 | 11.47 | 10.92★ | 10.92★ | 10.92★ | 9.95(464) |
| 2a0b_ | α | 118 | 4.25(1/6) | 12.76(3/9) | 4.25 | 13.22 | 13.22 | 13.22 | 13.22 | 9.90(63) |
| 2cdx_ | β | 60 | 6.98(7/16) | 3.61(1/7) | 3.61 | 3.61★ | 3.61★ | 3.61★ | 3.61★ | 3.04(913) |
| 2erl_ | α | 40 | 6.51(2/2) | 6.08(4/4) | 6.08 | 8.91 | 8.59 | 8.59 | 8.59 | 4.79(101) |
| 2hbg_ | α | 147 | 10.19(4/9) | 1.72(1/11) | 1.72 | 1.72★ | 1.72★ | 1.72★ | 1.72★ | 1.73(904) |
| 2i1b_ | β | 153 | 12.18(10/43) | 11.85(1/21) | 11.85 | 11.85 | 11.85 | 11.85 | 11.85 | 10.94(398) |
| 2mcm_ | β | 112 | 9.46(4/20) | 9.75(2/11) | 9.75 | 13.89 | 13.89 | 13.89 | 13.89 | 8.27(461) |
| 2sak_ | αβ | 121 | 9.17(9/29) | 11.23(12/24) | 11.86 | 11.86 | 11.25 | 14.19 | 11.25 | 8.02(913) |
| 3ebx_ | β | 62 | 7.35(3/26) | 2.24(1/15) | 2.24 | 2.24★ | 2.24★ | 2.24★ | 2.24★ | 1.53(734) |
| Average | 7.72(6.4/16.1) | 5.90(2.5/9.4) | 5.84 | 7.82 | 7.59 | 7.31 | 7.26 | 4.72(434) | ||
| Total number†††: | ||||||||||
| RMSD<6.5: | 42(41) | 83(83) | 85 | 58 | 60 | 65 | 67 | 94 | ||
| RMSD<6.0: | 31(29) | 75(75) | 77 | 55 | 57 | 61 | 63 | 92 | ||
| RMSD<5.5: | 22(21) | 69(69) | 71 | 51 | 55 | 57 | 59 | 89 | ||
| RMSD<5.0: | 15(14) | 64(64) | 66 | 48 | 50 | 53 | 55 | 83 | ||
| RMSD<4.5: | 11(10) | 55(55) | 56 | 42 | 43 | 46 | 47 | 77 | ||
| RMSD<4.0: | 7(7) | 41(41) | 44 | 36 | 35 | 38 | 38 | 69 | ||
| RMSD<3.5: | 3(3) | 29(29) | 31 | 27 | 26 | 29 | 28 | 61 | ||
| RMSD<3.0: | 2(2) | 22(22) | 24 | 21 | 20 | 22 | 22 | 42 |
*
PDB code of test proteins. The 30 proteins marked with ⋆ are those used in training for the force-field optimization.
†
The structure type assigned by DSSP (Kabsch and Sander, 1983).
‡
Protein length.
§
RMSD of the best cluster by the simulations without using protein-specific restraints. The first number in parentheses denotes the rank of the best cluster produced by SCAR (Betancourt and Skolnick, 2001), and the second number in parentheses is the total number of produced clusters. The cluster rank is obtained from the average energy of the structures in the cluster.
¶
RMSD of the best cluster by the simulation with the use of threading-based restraints by PROSPECTOR (Skolnick and Kihara, 2001). The first number in parentheses denotes the rank of the best cluster produced by SCAR, and the second number in parentheses is the total number of produced clusters. The cluster number is obtained from the average energy of the structures in the cluster.
‖
RMSD of the best cluster among the five combination clusters, i.e., the four lowest energy clusters from Clusterw plus the single lowest energy cluster from Clusterwo.
**
RMSD of the cluster centroid of the lowest energy E. ★ denotes that the lowest cluster is the cluster with the lowest RMSD to native.
††
RMSD of the cluster centroid of the biggest size M. ★ denotes that the biggest cluster is the cluster with the lowest RMSD to native.
‡‡
RMSD of the cluster centroid of the lowest Y. ★ denotes that the cluster of lowest Y is the cluster with the lowest RMSD to native.
§§
RMSD of the cluster centroid of the highest density D. ★ denotes that the cluster of highest density is the cluster with the lowest RMSD to native.
¶¶
RMSD of the best structure in the structure pool that is picked up from Monte Carlo trajectories and submitted to clustering processes. The number in parentheses is the number of MC steps when the best structure is produced.
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The 65-protein set that was used in our previous studies (Kihara et al., 2001; Zhang et al., 2002).
***
The 60 harder-protein set selected in the PISCES server (G. Wang and R. L. Dunbrack, unpublished results).
†††
The number of the proteins with RMSD below a threshold value. The number in parentheses is the number of the proteins if we only count the top five clusters.