Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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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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The JCSG MR pipeline: optimized alignments, multiple models and parallel searches.

(2008) Acta Crystallogr D Biol Crystallogr 64

PubMed: 18094477 | PubMedCentral: PMC2394805 | DOI: 10.1107/S0907444907050111

165 P 2 1 2 1 2 2 1.50 18.7 1g76 14     X 1vl7 tm1459, carbohydrate-binding protein, T. maritima 114 P 32 2 1.75 11.8 1lr5 18     X 1o5u tm1287, oxalate decarboxylase, ... . maritima 121 C 2 2 1.70 8.9 1vj2 18   X X 1o4t 15079298, glia maturation factor-γ, Mus musculus 142 P 1 1 1.35 15.7 1ahq 19 X X X 1vkk tm0603, 30s ribosomal protein s6, T. maritima 128 P 4 1 2 1 2 1 1.70 15.0 1lou 19     X 1vmb 17391249, haloacid dehalogenase-like hydrolase, M. musculus 248 P 6 1 22 1 1.90 12.0 1x42 19     X 2gfh tm1394, heat-shock protein 33, T. maritima 290 P 2 1 2 1 2 1 2 2.00 8.6 1i7f 20     X 1vq0 18044849, bifunctional coenzyme A synthase, M. musculus 269 C 2 1 1.70 15.0 1n3b 22     X 2f6r tm0820, NADH-dependent butanol dehydrogenase, T. maritima 395 P 2 1 2 1.78 10.0 1o2d 24     X 1vlj tm0332, orotidine 5′-phosphate decarboxylase, T. maritima 201 C 2 1 1.90 9.2 1eix 24     X 1vqt 10175646, BH3024 protein, Bacillus halodurans 126 P 4 1 2 1 2 1 2.40 6.5 1kgs 25 X X X 2b4a NP_394403, GMP synthase, T. acidophilum 212 P 2 1 2 1 2 4 2.45 4.4 1gdl 25     X 2a9v tm0262, DNA polymerase III, β subunit, T. maritima 366 P 4 2 2 1 2 1 2.70 4.8 1jqj 26     X 1vpk tm1419, myo -inositol-1-phosphate synthase, T. maritima 382 I 222 1 1.58 22.5 1gr0 26   X X 1vjp YP_290749.1, NADH dehydrogenase subunit C, T. fusca YX 252 P 4 3 2 1 2 1 2.60 8.6 2fug 27     X   tm1088A, hypothetical protein, T. maritima 143 P 2 1 1.50 20.3 1lss 27 X X X 2g1u tm0748, SAM-dependent O -methyltransferase, T. maritima 265 I 222 1 1.70 16.7 1i9g 28 X X X 1o54 tm0544, ABC transporter ATP-binding protein, T. maritima 244 P 3 1 2 1 1 2.10 10.6 1ji0 29     X 1vpl tm1128, ferritin, T. maritima 182 H 32 8 2.35 8.1 1eum 30 X X X 1vlg tm0295, transaldolase, T. maritima 218 P 2 1 20 2.40 5.1 1l6w 30     X 1vpx tm0343, DAHP synthase, T. maritima 338 P 2 1 2 1 2 1 3 1.90 8.5 1fwn 31 X X X 1vr6 tm1385, glucose-6-phosphate isomerase, T. maritima 448 I 2 1 2 1 2 1 3 2.90 6.8 1b0z 31   X X   tm1645, quinolinate phosphoribosyltransferase, T. maritima 273 I 222 2 2.80 6.9 1qpn 31     X 1o4u tm0066, 2-dehydro-3-deoxyphosphogluconate aldolase, T. maritima 205 C 222 1 3 2.30 6.8 1eua 31   X X 1vlw tm1393, MEP cytidylyltransferase, T. maritima 222 P 6 1 2 2.60 6.7 1vgz 31     X 1vpa tm1244, phosphoribosylformylglycinamidine synthase, T. maritima 82 I 4 1 22 4 2.50 7.0 1t4a 32     X 1vq3 tm0166, dihydrofolate synthase, T. maritima 430 P 6 1 22 1 2.75 8.9 1fgs 32 X X X 1o5z tm0919, hydroperoxide-resistance protein OsmC, T. maritima 138 P 2 1 4 1.80 12.9 1ml8 33     X 1vla tm1698, aspartate aminotransferase, T. maritima 397 P 2 1 6 2.50 4.1 1xi9 29 X X X 2gb3 tm0604, single-stranded DNA-binding protein, T. maritima 141 F 222 1 2.40 10.0 1qvc 34   X X 1z9f tm1169, 3-oxoacyl-(acyl carrier protein) reductase, T. maritima 237 P 2 1 2 1 2 1 4 2.50 4.3 1i01 34   X X 1o5i 17130499, anthranilate phosphoribosyltransferase 2, Nostoc sp.

Publication Year: 2008


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


ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

(2014) BMC Bioinformatics 15

PubMed: 25236673 | PubMedCentral: PMC4262145 | DOI: 10.1186/1471-2105-15-307

(A) 1SCP_ in I-TASSER, (B) 1CAU in Moulder, (C) 1LOU in Rosetta and (D) T0324 in CASP7.

Publication Year: 2014