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Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations.

(2009) BMC Struct Biol 9

PubMed: 19917096 | PubMedCentral: PMC2783033 | DOI: 10.1186/1472-6807-9-71

Table 6 Correlation between RMSD and residue-position Zscores Target Set C(ΔZ A E min ) C L (Z A E min ) C(ΔScZE min ) C L (ScZE min ) Average P/N Average P/N Average P/N Average P/N A... erage P/N Average P/N Average P/N Average P/N 1bbh 0.7 ± 0.1 124/34 0.7 ± 0.1 82/76 0.7 ± 0.1 135/23 0.7 ± 0.1 109/49 0.7 ± 0.1 112/46 0.6 ± 0.1 37/121 0.6 ± 0.1 92/66 0.7 ± 0.1 56/102 1c2r 0.7 ± 0.1 87/22 0.6 ± 0.2 25/84 0.7 ± 0.1 62/47 0.6 ± 0.2 23/36 0.5 ± 0.2 10/99 0.6 ± 0.2 13/96 0.5 ± 0.2 6/103 0.5 ± 0.2 5/104 1cau 0.6 ± 0.2 22/16 0.7 ± 0.2 28/10 0.5 ± 0.2 4/34 0.7 ± 0.2 28/10 0.6 ± 0.2 11/27 0.7 ± 0.2 26/12 0.5 ± 0.2 7/31 0.6 ± 0.2 19/19 1cew 0.8 ± 0.0 1/11 0.5 ± 0.3 3/9 0.6 ± 0.0 1/11 0.8 ± 0.0 1/11 0.6 ± 0 1/11 0.5 ± 0.4 2/10 0.0 ± 0.0 0/12 0.8 ± 0.0 1/11 1cid 0.7 ± 0.1 56/27 0.8 ± 0.2 52/31 0.7 ± 0.1 60/23 0.7 ± 0.1 59/24 0.8 ± 0.1 77/6 0.7 ± 0.2 28/55 0.8 ± 0.1 80/3 0.7 ± 0.2 28/55 1dxt 0.6 ± 0.1 44/106 0.7 ± 0.1 89/61 0.6 ± 0.1 79/71 0.7 ± 0.1 111/39 0.5 ± 0.2 6/144 0.7 ± 0.2 46/104 0.5 ± 0.2 8/142 0.7 ± 0.1 56/94 1eaf 0.5 ± 0.2 10/50 0.6 ± 0.2 18/42 0.6 ± 0.2 15/45 0.5 ± 0.1 22/38 0.4 ± 0.2 3/57 0.6 ± 0.2 17/43 0.4 ± 0.2 3/57 0.6 ± 0.1 28/32 1gky 0.6 ± 0.2 12/17 0.7 ± 0.2 14/5 0.5 ± 0.2 5/14 0.6 ± 0.2 14/5 0.6 ± 0.2 13/6 0.6 ± 0.2 10/9 0.6 ± 0.2 13/6 0.7 ± 0.2 12/7 1lga 0.5 ± 0.2 12/95 0.5 ± 0.2 10/97 0.5 ± 0.2 9/98 0.5 ± 0.2 5/102 0.6 ± 0.0 1/106 0.5 ± 0.2 8/99 0.4 ± 0.3 2/105 0.4 ± 0.3 3/104 1mdc 0.7 ± 0.1 59/56 0.7 ± 0.2 42/73 0.7 ± 0.1 68/47 0.7 ± 0.2 47/68 0.6 ± 0.1 39/76 0.6 ± 0.1 28/87 0.6 ± 0.2 16/99 0.6 ± 0.2 18/97 1mup 0.7 ± 0.1 60/74 0.7 ± 0.1 73/61 0.7 ± 0.1 68/66 0.7 ± 0.1 77/57 0.7 ± 0.1 99/35 0.7 ± 0.1 59/75 0.7 ± 0.1 112/22 0.7 ± 0.1 53/81 1onc 0.7 ± 0.2 53/69 0.6 ± 0.2 29/93 0.7 ± 0.2 59/63 0.7 ± 0.2 38/84 0.7 ± 0.1 102/20 0.7 ± 0.2 43/79 0.7 ± 0.1 86/36 0.7 ± 0.1 40/82 2afn 0.6 ± 0.1 80/39 0.6 ± 0.1 73/46 0.6 ± 0.1 22/97 0.6 ± 0.1 71/48 0.5 ± 0.1 25/94 0.5 ± 0.2 18/103 0.5 ± 0.2 9/110 0.5 ± 0.1 17/102 2cmd 0.7 ± 0.1 101/128 0.6 ± 0.1 112/117 0.6 ± 0.1 93/136 0.6 ± 0.1 103/126 0.6 ± 0.1 102/127 0.6 ± 0.1 50/179 0.6 ± 0.1 42/187 0.6 ± 0.1 58/171 2fbj 0.6 ± 0.2 12/89 0.6 ± 0.1 24/77 0.6 ± 0.2 7/94 0.6 ± 0.2 13/88 0.6 ± 0.1 32/69 0.6 ± 0.2 11/90 0.6 ± 0.1 40/61 0.6 ± 0.1 19/82 2mta 0.6 ± 0.1 47/111 0.7 ± 0.1 48/110 0.7 ± 0.1 75/83 0.7 ± 0.2 32/126 0.7 ± 0.1 104/54 0.7 ± 0.1 73/85 0.7 ± 0.1 130/28 0.6 ± 0.2 40/118 2pna 0.7 ± 0.1 41/97 0.7 ± 0.1 73/65 0.7 ± 0.2 37/101 0.7 ± 0.1 71/67 0.0 ± 0.0 0/138 0.7 ± 0.2 67/71 0.6 ± 0.2 12/126 0.7 ± 0.2 59/79 2sim 0.5 ± 0.2 4/90 0.4 ± 0.3 3/91 0.0 ± 0.0 0/94 0.6 ± 0.0 1/93 0.4 ± 0.3 2/92 0.6 ± 0.0 1/93 0.4 ± 0.3 2/92 0.0 ± 0.0 0/94 4sbv 0.5 ± 0.4 2/2 0.4 ± 0.3 2/2 0.4 ± 0.3 2/2 0.4 ± 0.3 2/2 0.0 ± 0.0 0/4 0.0 ± 0.0 0/4 0.0 ± 0.0 0/4 0.0 ± 0.0 0/4 8i1b 0.4 ± 0.3 2/135 0.6 ± 0.2 11/126 0.5 ± 0.2 5/132 0.6 ± 0.2 13/124 0.6 ± 0.1 43/94 0.5 ± 0.1 18/119 0.5 ± 0.1 23/114 0.6 ± 0.2 13/124 Pearson correlation between RMSD of C α atoms and residue-position Zscores of structure-models in MOULDER decoy set.

Target ZE min ZE Aa3DEnv -min ZE 3DEnv -min ZE local -min 1bbh 0.86 0.36 -0.83 -0.80 0.62 0.42 -0.02 -0.71 1c2r 0.71 0.45 -0.48 -0.67 0.69 0.68 -0.43 -0.27 1cau 0.83 0.56 -0.71 -0.72 0.69 0.38 -0.40 -0.74 1cew 0.70 0.31 -0.64 -0.58 0.61 0.08 -0.18 -0.63 1cid 0.41 -0.12 -0.22 -0.59 0.45 0.43 0.10 -0.55 1dxt 0.87 0.75 -0.84 -0.76 0.78 0.76 -0.51 -0.51 1eaf 0.79 0.57 -0.61 -0.64 0.72 0.66 -0.38 -0.55 1gky 0.88 0.54 -0.77 -0.78 0.73 0.61 -0.18 -0.63 1lga 0.88 0.49 -0.68 -0.85 0.84 0.68 -0.40 -0.84 1mdc 0.78 0.50 -0.51 -0.64 0.68 0.40 -0.20 -0.60 1mup 0.85 0.66 -0.80 -0.83 0.80 0.79 0.24 -0.79 1onc 0.78 0.66 -0.58 -0.58 0.80 0.75 -0.29 -0.56 2afn 0.86 0.61 -0.60 -0.83 0.77 0.68 -0.27 -0.83 2cmd 0.81 0.68 -0.82 -0.78 0.63 0.58 -0.46 -0.65 2fbj 0.77 0.35 -0.32 -0.82 0.79 0.58 -0.13 -0.83 2mta 0.72 0.47 -0.16 -0.69 0.77 0.67 -0.02 -0.70 2pna 0.83 0.58 -0.79 -0.55 0.62 0.52 -0.29 -0.46 2sim 0.81 -0.12 -0.73 -0.81 0.66 0.20 -0.36 -0.76 4sbv 0.69 -0.10 -0.65 -0.60 0.54 0.46 -0.07 -0.45 8i1b 0.77 0.68 -0.36 -0.60 0.57 0.67 0.13 -0.43 Pearson product-correlation between Root Mean Square Deviation (RMSD) of MOULDER decoys of 20 target/model sets (in rows) and Zscores (in columns): , , , , ZE min , ZE S3DC -min , ZE 3DC -min , and ZE local -min .

Target set DOPE GA341 Prosa2003 DFIRE ZEmin fisa_casp3 1eh2 6,06 4,64 1,64 4,93 4,13 4,93 1bg8 -A 7,84 7,28 7,28 3,58 5,72 3,58 1jwe 6,30 10,62 9,75 8,10 9,52 8,10 1bl0 4,10 2,24 2,24 7,10 4,45 7,10 smd3 4,35 6,44 5,08 5,12 5,32 4,47 Average 5,73 6,25 5,20 5,76 5,83 5,63 lmds 1dtk 5,46 4,75 4,59 4,59 4,89 2,90 1igd 7,64 1,63 4,28 5,61 4,50 5,61 2cro 8,68 8,95 6,14 10,01 5,93 9,48 smd3 4,35 4,52 2,68 5,52 2,50 5,52 1ctf 9,41 7,65 7,52 7,37 6,67 7,37 1fc2 0,26 0,51 1,00 0,07 1,51 0,07 1shf -A 5,83 5,16 3,06 6,91 5,24 6,91 4pti 5,64 5,72 9,91 4,61 9,54 4,61 2ovo 6,92 3,49 6,45 5,70 7,26 5,70 1b0n -B 1,60 2,20 0,61 0,50 1,76 0,50 1bba 1,89 0,87 0,59 3,29 2,00 1,92 Average 5,24 4,13 4,26 4,92 4,71 4,60 4state_reduced 1sn3 1,69 0,90 4,09 4,71 6,05 0,90 1r69 2,55 0,80 0,79 0,95 2,29 0,79 4pti 0,82 5,53 0,07 0,07 1,18 2,80 2cro 2,46 1,24 0,29 1,24 0,53 0,53 1ctf 0,33 0,60 0,50 2,93 1,02 1,02 3icb 1,86 1,51 0,93 0,11 0,05 0,11 4rxn 0,46 3,52 0,75 0,70 0,68 0,70 Average 1,45 2,01 1,06 1,53 1,69 0,98 MOULDER 1onc 1,16 0,72 0,60 0,40 0,40 0,40 1dxt 3,97 0,00 0,55 1,11 0,00 0,55 1eaf 0,34 1,72 1,72 0,47 0,99 0,47 1lga 0,82 5,89 5,89 0,80 0,00 0,80 1gky 0,57 0,34 0,57 0,57 0,62 0,57 1cau 3,89 1,95 0,42 0,42 0,07 0,42 4sbv 0,00 5,57 0,00 0,00 6,43 0,00 8i1b 0,38 0,42 0,39 0,50 0,36 1,04 2mta 0,31 0,57 0,21 0,63 0,32 0,63 2cmd 0,38 2,22 0,58 0,23 0,74 0,84 2fbj 0,26 2,80 0,32 0,91 0,51 0,91 1cew 2,06 2,73 2,73 3,47 3,73 3,47 2afn 0,71 0,75 0,68 0,12 0,50 0,12 2sim 1,21 0,42 0,46 0,16 1,13 0,16 1bbh 0,88 0,11 0,16 0,00 0,31 0,00 1mdc 0,03 0,74 6,85 0,16 0,00 0,16 1mup 0,53 0,17 0,67 0,67 0,32 0,46 2pna 0,26 0,60 0,42 0,24 0,26 0,24 1cid 1,15 1,15 1,15 0,08 1,15 1,15 1c2r 3,42 0,00 0,85 0,00 0,00 0,15 Average 1,12 1,44 1,26 0,55 0,89 0,63 In the first column it is shown the code of the target protein used to generate the set of decoys.

Target set DOPE GA341 Prosa2003 DFIRE ZEmin fisa_casp3 smd3 1 51 2 1 12 1 1bg8 -A 1 808 151 1 341 2 1jwe 1 135 4 1 514 1 1eh2 8 826 93 1 577 159 1bl0 1 809 729 1 458 3 Total 4 0 0 5 0 2 lmds smd3 1 15 1 1 1 1 2ovo 7 33 1 61 115 7 1dtk 1 1 1 1 77 33 4pti 6 7 1 24 25 10 1b0n -B 293 35 1 418 99 180 1bba 501 395 458 501 389 63 1shf -A 1 5 13 1 199 1 1ctf 1 1 1 1 1 1 1fc2 501 234 107 501 276 489 1igd 1 1 1 18 10 1 2cro 1 10 1 1 43 16 Total 6 3 8 5 2 4 4state_reduced 4rxn 1 1 8 1 20 26 4pti 1 6 1 1 1 1 1ctf 1 1 1 1 1 1 3icb 3 5 1 5 10 9 1sn3 1 1 1 1 25 3 2cro 1 5 1 1 1 2 1r69 1 4 1 1 1 1 Total 6 3 6 6 4 3 MOULDER 1onc 1 1 1 1 1 1 1dxt 1 1 1 1 3 1 1eaf 1 1 1 1 1 1 1lga 1 1 1 1 1 1 1gky 1 1 1 1 1 1 1cau 1 1 1 1 1 1 4sbv 1 1 1 1 1 1 8i1b 1 1 1 1 1 1 2mta 1 1 1 1 4 4 2fbj 1 1 1 1 1 1 2cmd 1 1 1 1 1 1 1cew 1 1 1 1 1 1 2afn 1 1 1 1 1 1 2sim 1 1 1 1 1 1 1bbh 1 1 1 1 1 1 1mdc 1 1 1 1 1 1 1mup 1 1 1 1 15 1 2pna 85 45 43 85 58 9 1cid 1 1 1 1 1 1 1c2r 1 1 1 1 6 1 Total 19 19 19 19 15 18 Ranking position of the native structure among the sets of model/target decoys for several scoring functions.

Publication Year: 2009