Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 5

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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Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.

(2007) BMC Struct Biol 7

PubMed: 17397537 | PubMedCentral: PMC1852318 | DOI: 10.1186/1472-6807-7-19

Among unrecognized structures, e.g. 1ptq has a large hydrophobic patch at its surface and lacks a clearly defined hydrophobic core, whereas 1a32 has a loose packing with a number of hydrophobic groups... accessible to the solvent.

Publication Year: 2007


Prospects for de novo phasing with de novo protein models.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19171972 | PubMedCentral: PMC2631639 | DOI: 10.1107/S0907444908020039

of models, large-scale ¶ Low-resolution models, 100 CPU days †† All-atom models, 100 CPU days †† All-atom models, large-scale †† Models, native ... onstraints ‡‡ Overall §§ 1be7 1bq9 H 3 51 1 43 3.5 × 10 5 1.7 × 10 7 — — — 0.882 0.882 1bq9 1bq9 P 2 1 2 1 2 1 51 1 43 3.5 × 10 5 1.7 × 10 7 — — — 0.627 0.627 2igd 1pgx P 2 1 2 1 2 1 55 1 46 2.7 × 10 5 4.2 × 10 5 — — 0.745 0.891 0.709 5cro 5cro H 32 55 4 70 2.6 × 10 5 7.4 × 10 5 — — 0.927 0.982 0.709 1hz5 1hz6 P 3 2 21 61 2 72 2.3 × 10 5 7.3 × 10 5 — 0.541 0.656 0.787 0.541 1hz6 1hz6 P 2 1 2 1 2 1 61 3 59 2.3 × 10 5 7.3 × 10 5 — 0.672 0.689 0.836 0.639 1a32 1a32 P 2 1 2 1 2 1 65 1 41 2.8 × 10 5 2.8 × 10 5 — 0.754 0.708 0.800 0.677 1ctf 1ctf P 4 3 2 1 2 68 1 47 2.4 × 10 5 3.2 × 10 5 — — — 0.882 0.515 1aar 1ubi P 1 71 2 35 2.0 × 10 5 5.4 × 10 7 — — — — 1.000 1f9j 1ubi I 4 1 22 71 2 60 2.0 × 10 5 5.4 × 10 7 — — — — 0.901 1ubq 1ubi P 2 1 2 1 2 1 71 1 33 2.0 × 10 5 5.4 × 10 7 — — 0.690 0.662 0.549 2fcq 1ubi P 4 3 32 71 2 58 2.0 × 10 5 5.4 × 10 7 — — — — 0.915 2ojr 1ubi P 3 2 21 71 1 73 2.0 × 10 5 5.4 × 10 7 — — — 0.549 0.549 1dt4 1dtj P 4 2 2 1 2 74 1 54 2.8 × 10 5 4.9 × 10 5 0.649 0.622 0.500 0.635 0.419 1dtj 1dtj C 2 74 4 60 2.8 × 10 5 4.9 × 10 5 — 0.635 0.716 0.811 0.635 1ig5 1ig5 P 4 3 2 1 2 75 1 43 2.3 × 10 5 8.3 × 10 6 — — — 0.307 0.307 1cm3 1opd P 2 1 85 1 28 2.3 × 10 5 8.4 × 10 6 — — — 0.753 0.459 1opd 1opd P 1 85 1 33 2.3 × 10 5 8.4 × 10 6 — — — 0.800 0.800 1a19 1a19 I 4 1 89 2 49 1.7 × 10 5 7.0 × 10 6 — — — 0.494 0.494 2hxx 1a19 C 2 89 2 46 1.7 × 10 5 7.0 × 10 6 — — — 0.674 0.674 1mb1 1bm8 P 4 1 2 1 2 99 1 51 1.6 × 10 5 9.2 × 10 5 — — — — 0.747 2hsh 1aiu C 2 105 1 35 1.5 × 10 5 4.4 × 10 5 — — 0.400 0.600 0.400 1m6t 256b C 222 1 106 1 43 1.8 × 10 5 1.5 × 10 5 — 0.453 0.443 0.491 0.283 256b 256b P 1 106 2 45 1.8 × 10 5 1.5 × 10 5 — — 0.660 0.594 0.585 2bc5 256b P 2 1 2 1 2 1 106 4 42 1.8 × 10 5 1.5 × 10 5 — 0.538 — 0.689 0.538 1elw 1elw P 4 1 117 2 47 1.5 × 10 5 1.1 × 10 5 — 0.453 0.521 0.897 0.436 1ab6 2chf P 3 1 128 2 57 1.2 × 10 5 3.5 × 10 6 — — 0.508 0.398 0.398 2fka 2chf F 432 128 1 79 1.2 × 10 5 3.5 × 10 6 — 0.430 0.359 0.367 0.313 3chy 2chf P 2 1 2 1 2 1 128 1 41 1.2 × 10 5 3.5 × 10 6 — — — 0.492 0.320 6chy 2chf P 2 1 2 1 2 1 128 2 43 1.2 × 10 5 3.5 × 10 6 — — 0.398 0.422 0.398 † F 1 Å is a measure of model accuracy: the fraction of C α atoms within 1 Å of the crystal structure of the modeled sequence.

Publication Year: 2009


PDBWiki: added value through community annotation of the Protein Data Bank.

(2010) Database (Oxford) 2010

PubMed: 20624717 | PubMedCentral: PMC2911844 | DOI: 10.1093/database/baq009

Learning about the studies that a particular structure has been used in (see for example, user annotations for entry 1a32).

Publication Year: 2010


Structure prediction for the helical skeletons detected from the low resolution protein density map.

(2010) BMC Bioinformatics 11 Suppl 1

PubMed: 20122218 | PubMedCentral: PMC3009517 | DOI: 10.1186/1471-2105-11-S1-S44

Table 1 The test of the structure prediction for the helical skeletons No ID #AA a #hlces b #sticks c #Possible Topologies d #Valid Topologies e #Generated structures f Rank g RMSD h Prct i 1 1DP3 55 ... 3 48 6 3000 10 4.78 0.33% 2 1A2T 149 3 3 48 32 16000 15 3.72 0.09% 3 1AIL 73 3 3 48 16 8000 3 3.96 0.04% 4 1BUU 168 3 3 48 16 8000 27 4.67 0.34% 5 1lRE 81 3 3 48 18 9000 10 4.55 0.11% 6 1BR0 120 3 3 48 4 2000 4 11.17 0.20% 7 1B67 68 3 3 48 14 7000 17 4.03 0.24% 8 1AYI 87 4 3 192 48 24000 93 3.8 0.39% 9 1BEA 127 4 3 192 160 80000 572 4.75 0.72% 10 1GXG 85 4 3 192 40 20000 12 2.8 0.06% 11 1NO1 126 4 3 192 120 60000 42 4.24 0.07% 12 2EZH 75 4 3 192 104 52000 47 4.2 0.09% 13 1A3C 181 4 3 192 48 24000 110 3.57 0.46% 14 1A32 88 4 3 192 40 20000 9 3.69 0.05% 15 1PZ4 116 4 3 192 72 36000 147 7.3 0.41% 16 1LIH 164 4 3 192 124 62000 114 5.48 0.18% 17 1DXS 80 5 3 480 450 225000 30 3.51 0.01% 18 1SU0 159 5 3 480 96 48000 60 6.69 0.13% 19 1BO9 73 6 3 960 438 219000 35 3.43 0.02% 20 1JW2 72 4 4 384 66 33000 31 4.26 0.09% 21 1I2T 61 4 4 384 64 32000 21 5.58 0.07% 22 1CCD 77 4 4 384 20 10000 3 4.75 0.03% 23 2PSR 100 5 4 1920 468 234000 339 4.75 0.14% 24 1A7D 118 6 4 5760 139 69500 144 5.33 0.21% 25 2LIS 136 6 4 5760 144 72000 8 4.84 0.01% 26 1ALU 186 6 4 5760 419 209500 288 7.22 0.14% 27 1HXI 121 6 4 5760 400 200000 17 3.78 0.01% 28 1JMW 146 6 4 5760 304 152000 129 5.25 0.08% 29 1AA2 108 7 4 13440 768 384000 3599 4.15 0.94% 30 1BVC 153 8 4 26880 1215 607500 8 5.59 0.00% 31 1BZ4 144 5 5 3840 16 8000 31 4.91 0.39% 32 1AEP 161 5 5 3840 157 78500 204 5.3 0.26% 33 1DUS 194 6 5 23040 3840 1920000 2179 4.44 0.11% 34 1B5L 172 6 5 23040 438 219000 759 5.44 0.35% 35 1FLP 142 7 6 322560 7734 3867000 4707 4.65 0.12% a: the number of amino acids in the protein b: the number of helices in the protein c: the number of skeletons detected by Helix Tracer d: the number of all possible topologies e: the number of valid topologies after applying distance and length screening f: the number of structures generated for all valid topologies g: the highest rank of the structure that has the correct topology h: the Root Mean Square Deviation (RMSD) of Cá atoms of the structure that has the highest rank with the correct topology i: the percentage of the highest rank among all generated structures Figure 2 The highest ranked structure with the correct topology for 1B5L (PDB ID) .

Publication Year: 2010


Use of a structural alphabet for analysis of short loops connecting repetitive structures.

(2004) BMC Bioinformatics 5

PubMed: 15140270 | PubMedCentral: PMC450294 | DOI: 10.1186/1471-2105-5-58

Example of 5 assignments for the ribosomal protein S15 from Bacillus Stearothermophilus (PDB code 1A32).

Example of the ribosomal protein S15 from Bacillus Stearothermophilus (PDB code 1A32) with (a) DSSP, (b) STRIDE, (c) PSEA, (d) DEFINE, (e) PCURVE and (f) Protein Blocks.

Figures 2 and 3 use the example of the ribosomal protein S15 from Bacillus Stearothermophilus (PDB code 1A32; another example, proto-oncogene Mtcp-1, PDB code 1A1X, is given [see Additional file 1 and Additional file 2 ]) to show the multiple secondary structure assignments that can ensue.

Publication Year: 2004