Citations in PubMed

Primary Citation PubMed: 1618774 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Scoring predictive models using a reduced representation of proteins: model and energy definition.

(2007) BMC Struct Biol 7

PubMed: 17378941 | PubMedCentral: PMC1854906 | DOI: 10.1186/1472-6807-7-15

rank native RMSD Z-score cc F.E. hg_structal 1ash 1/30 0.0 -2.0 0.62 66.7 hg_structal 1bab-B 3/30 0.8 -1.4 0.83 66.7 hg_structal 1col-A 1/30 0.0 -4.8 0.73 33.3 hg_structal 1cpc-A 1/30 0.0 -3.4 0.61 33... 3 hg_structal 1ecd 28/30 1.5 1.8 0.57 33.3 hg_structal 1emy 3/30 0.8 -1.9 0.81 100.0 hg_structal 1flp 3/30 1.9 -1.5 0.44 33.3 hg_structal 1gdm 1/30 0.0 -3.0 0.82 100.0 hg_structal 1hbg 1/30 0.0 -2.2 0.54 33.3 hg_structal 1hbh-A 2/30 1.1 -1.6 0.87 33.3 hg_structal 1hbh-B 5/30 1.0 -1.1 0.80 33.3 hg_structal 1hda-A 2/30 0.5 -1.5 0.92 66.7 hg_structal 1hda-B 1/30 0.0 -1.4 0.84 100.0 hg_structal 1hlb 9/30 2.9 -0.4 0.55 33.3 hg_structal 1hlm 30/30 4.0 2.3 0.21 33.3 hg_structal 1hsy 5/30 0.9 -1.3 0.82 66.7 hg_structal 1ith-A 1/30 0.0 -2.6 0.78 66.7 hg_structal 1lht 30/30 0.8 3.0 0.41 66.7 hg_structal 1mba 1/30 0.0 -1.7 0.72 33.3 hg_structal 1mbs 30/30 1.8 2.2 0.52 66.7 hg_structal 1myg-A 1/30 0.0 -2.0 0.82 66.7 hg_structal 1myj-A 2/30 0.6 -1.8 0.86 66.7 hg_structal 1myt 1/30 0.0 -2.3 0.72 66.7 hg_structal 2dhb-A 8/30 0.8 -0.8 0.85 66.7 hg_structal 2dhb-B 8/30 1.0 -0.7 0.83 66.7 hg_structal 2lhb 1/30 0.0 -2.6 0.71 33.3 hg_structal 2pgh-A 5/30 1.0 -1.2 0.91 33.3 hg_structal 2pgh-B 7/30 0.8 -0.8 0.85 33.3 hg_structal 4sdh-A 1/30 0.0 -3.6 0.70 33.3 Table 5 Performance evaluation of the energy function on ig_structal decoy set Decoy set PDB id.

Publication Year: 2007


A knowledge-based structure-discriminating function that requires only main-chain atom coordinates.

(2008) BMC Struct Biol 8

PubMed: 18957132 | PubMedCentral: PMC2600639 | DOI: 10.1186/1472-6807-8-46

protein N R nat C α RMSD Z-score C.C. F.E.(%) R B1 logP B1 R B10 logP B10 C.C. decoy F.E. decoy (%) 4state_reduced 1ctf 631 1 0.000 4.485 0.817 68.3 61 -1.01 3 -2.32 0.815 66.7 2cro 675 1 0.00... 3.166 0.822 53.7 7 -1.98 2 -2.53 0.820 53.7 4rxn 678 1 0.000 2.895 0.670 65.7 71 -0.98 3 -2.35 0.665 64.2 Average 661.3 1.0 0.000 3.515 0.770 62.6 46.3 -1.33 2.7 -2.40 0.767 61.5 fisa 2cro 501 1 0.000 4.190 0.280 24.0 3 -2.22 2 -2.40 0.253 24.0 Average 501.0 1.0 0.000 4.190 0.280 24.0 3.0 -2.22 2.0 -2.40 0.253 24.0 fisa_casp3 1bl0 972 8 5.522 2.174 0.302 20.6 15 -1.81 15 -1.81 0.296 19.6 l30 1401 1 1.882 3.835 0.128 18.6 455 -0.49 3 -2.67 0.111 17.9 Average 1186.5 4.5 3.702 3.005 0.215 19.6 235.0 -1.15 9.0 -2.24 0.204 18.7 hg_structal 1bab-B 30 1 0.000 1.868 0.904 66.7 10 -0.46 2 -1.16 0.892 0.0 1ecd 30 1 0.000 1.364 0.896 100.0 2 -1.16 2 -1.16 0.898 50.0 1gdm 30 1 0.000 2.395 0.880 33.3 4 -0.86 2 -1.16 0.845 0.0 1hbh-B 30 1 0.000 1.205 0.893 33.3 6 -0.68 2 -1.16 0.888 0.0 1hlb 30 1 0.000 1.661 0.812 33.3 15 -0.29 2 -1.16 0.812 0.0 1ith-A 30 1 0.000 1.775 0.904 33.3 23 -0.10 2 -1.16 0.893 0.0 1mbs 30 18 1.823 -0.270 0.754 33.3 3 -0.99 2 -1.16 0.835 0.0 1myt 30 1 0.000 2.429 0.762 100.0 2 -1.16 2 -1.16 0.725 50.0 2lhb 30 1 0.000 1.976 0.563 33.3 12 -0.38 4 -0.86 0.460 0.0 4sdh-A 30 1 0.000 3.221 0.839 33.3 21 -0.14 2 -1.16 0.750 0.0 Average 30.0 2.7 0.182 1.762 0.821 50.0 9.8 -0.62 2.2 -1.13 0.800 10.0 ig_structal 1bbd 61 1 0.000 2.304 0.605 16.7 27 -0.35 10 -0.78 0.554 0.0 1dfb 61 7 1.854 0.864 0.530 16.7 12 -0.70 4 -1.18 0.528 16.7 1fai 61 4 1.736 1.172 0.481 16.7 13 -0.66 4 -1.18 0.462 0.0 1fig 61 59 1.702 -2.283 0.349 0.0 21 -0.46 6 -1.00 0.504 0.0 1fpt 61 2 1.333 1.358 0.583 33.3 8 -0.88 4 -1.18 0.565 16.7 1fvd 61 1 0.000 2.112 0.606 16.7 22 -0.44 2 -1.48 0.574 0.0 1gig 61 1 0.000 2.787 0.547 16.7 10 -0.78 10 -0.78 0.469 0.0 1iai 61 1 0.000 2.103 0.644 33.3 8 -0.88 2 -1.48 0.613 16.7 1igf 61 2 1.774 1.353 0.607 16.7 31 -0.29 8 -0.88 0.591 0.0 1ikf 61 1 0.000 2.561 0.592 33.3 8 -0.88 3 -1.30 0.540 16.7 1jhl 61 1 0.000 1.380 0.333 16.7 41 -0.17 5 -1.08 0.286 0.0 1mcp 61 1 0.000 2.143 0.623 66.7 3 -1.30 2 -1.48 0.585 50.0 1mrd 61 1 0.000 2.305 0.379 16.7 51 -0.07 7 -0.93 0.264 0.0 1ngq 61 1 0.000 2.716 0.543 33.3 2 -1.48 2 -1.48 0.456 16.7 1opg 61 1 0.000 2.175 0.575 33.3 44 -0.14 3 -1.30 0.529 33.3 1tet 61 1 0.000 2.323 0.567 33.3 4 -1.18 4 -1.18 0.523 16.7 1vge 61 1 0.000 2.766 0.208 16.7 45 -0.13 26 -0.36 -0.020 0.0 2fb4 61 1 0.000 2.277 0.486 16.7 32 -0.27 13 -0.66 0.422 0.0 3hfl 61 1 0.000 2.648 0.243 33.3 29 -0.32 4 -1.18 0.055 16.7 7fab 61 1 0.000 2.941 0.614 50.0 6 -1.00 3 -1.30 0.531 33.3 Average 61.0 4.5 0.420 1.900 0.506 25.8 20.9 -0.62 6.1 -1.11 0.452 11.7 ig_structal_hires 1fgv 20 1 0.000 2.310 0.724 50.0 6 -0.50 2 -0.98 0.633 0.0 1gaf 20 1 0.000 2.827 0.649 50.0 8 -0.38 2 -0.98 0.493 0.0 1kem 20 1 0.000 1.518 0.636 50.0 11 -0.24 3 -0.80 0.567 0.0 1nbv 20 10 1.719 0.169 0.399 0.0 7 -0.43 4 -0.68 0.452 0.0 1vge 20 1 0.000 2.334 0.385 50.0 15 -0.10 2 -0.98 -0.116 0.0 2fbj 20 1 0.000 2.532 0.725 50.0 5 -0.58 2 -0.98 0.614 0.0 8fab 20 1 0.000 2.487 0.295 50.0 17 -0.05 8 -0.38 -0.228 0.0 Average 20.0 2.3 0.246 2.025 0.545 42.9 9.9 -0.33 3.3 -0.82 0.345 0.0 lattice_ssfit 1dkt-A 1995 1 0.000 7.349 -0.049 8.5 996 -0.30 242 -0.92 -0.087 8.0 1pgb 1997 1 0.000 13.649 0.138 17.1 1909 -0.02 60 -1.52 0.087 16.6 Average 1996.0 1.0 0.000 10.499 0.045 12.8 1452.5 -0.16 151.0 -1.22 0.000 12.3 lmds 1b0n-B 498 1 0.000 2.819 0.066 20.4 336 -0.17 10 -1.70 0.038 18.4 1dtk 216 70 7.224 0.375 0.044 4.8 42 -0.71 24 -0.95 0.038 4.8 1shf-A 437 1 0.000 4.275 0.064 11.6 378 -0.06 2 -2.34 -0.004 9.3 4pti 344 3 9.434 2.570 0.098 23.5 220 -0.19 4 -1.93 0.063 20.6 Average 373.8 18.8 4.165 2.510 0.068 15.1 244.0 -0.28 10.0 -1.73 0.034 13.3 semfold 1eh2 11442 61 12.125 2.342 0.070 13.6 6511 -0.25 434 -1.42 0.069 13.5 1pgb 11282 1 0.000 7.782 0.096 19.2 2 -3.75 2 -3.75 0.091 19.2 Average 11362.0 31.0 6.063 5.062 0.083 16.4 3256.5 -2.00 218.0 -2.59 0.080 16.3 moulder 1c2r 301 1 0.000 2.803 0.774 73.3 10 -1.48 2 -2.18 0.768 70.0 1cid 301 1 0.000 2.759 0.753 53.3 38 -0.90 2 -2.18 0.748 53.3 1gky 300 1 0.000 4.713 0.828 90.0 11 -1.43 3 -2.00 0.819 89.7 1mup 301 1 0.000 1.993 0.847 73.3 11 -1.44 3 -2.00 0.845 73.3 2cmd 301 1 0.000 2.506 0.911 36.7 15 -1.30 6 -1.70 0.911 33.3 2pna 301 85 3.523 0.723 0.816 66.7 30 -1.00 4 -1.88 0.817 66.7 8i1b 301 1 0.000 2.106 0.842 46.7 16 -1.27 4 -1.88 0.840 46.7 Average 300.9 13.0 0.503 2.515 0.824 62.9 18.7 -1.26 3.4 -1.97 0.821 61.9 rosetta 1a68 141 1 0.000 2.608 0.624 64.3 11 -1.11 3 -1.67 0.608 64.3 1aiu 141 15 1.385 0.805 0.777 7.1 40 -0.54 25 -0.75 0.776 7.1 1bk2 141 1 0.000 2.562 0.820 78.6 14 -1.00 3 -1.67 0.812 78.6 1bq9 141 2 9.242 1.895 0.544 50.0 131 -0.03 2 -1.85 0.532 50.0 1cc8 141 1 0.000 3.317 0.848 64.3 11 -1.11 2 -1.85 0.851 57.1 1ctf 141 1 0.000 4.288 0.783 28.6 30 -0.67 6 -1.37 0.780 28.6 1elw 141 22 3.619 1.082 -0.063 7.1 132 -0.03 12 -1.07 -0.070 7.1 1eyv 141 1 0.000 3.194 0.587 35.7 22 -0.80 2 -1.85 0.564 35.7 1gvp 141 1 0.000 3.018 0.540 21.4 61 -0.36 15 -0.97 0.514 21.4 1iib 141 1 0.000 6.093 0.595 71.4 9 -1.19 2 -1.85 0.629 71.4 1lou 141 1 0.000 2.664 0.741 71.4 8 -1.24 3 -1.67 0.731 64.3 1pgx 141 1 0.000 2.232 0.821 35.7 75 -0.27 5 -1.45 0.820 28.6 1rnb 141 8 13.461 1.445 0.440 21.4 89 -0.20 14 -1.00 0.427 21.4 1ten 141 1 0.000 4.986 0.866 92.9 5 -1.45 2 -1.85 0.876 85.7 1tul 141 5 0.842 2.002 0.763 64.3 16 -0.94 3 -1.67 0.755 57.1 1urn 141 1 0.000 2.452 0.694 64.3 9 -1.19 3 -1.67 0.680 57.1 1vie 141 1 0.000 3.470 0.791 71.4 2 -1.85 2 -1.85 0.781 71.4 256b 141 1 0.000 4.974 0.426 7.1 118 -0.07 42 -0.52 0.390 0.0 2ci2 141 80 10.219 0.075 -0.020 0.0 123 -0.06 71 -0.30 -0.022 0.0 Average 141.0 7.6 2.040 2.798 0.609 45.1 47.7 -0.74 11.4 -1.41 0.602 42.5 The performance scores for respective PDB IDs of the target proteins and their average are shown by individual generation methods.

Publication Year: 2008