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PDB ID Mentions in PubMed Central Article count: 4

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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Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-secreted periplasmic protein with a potential role in iron transport.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63

PubMed: 17183171 | PubMedCentral: PMC2330106 | DOI: 10.1107/S174430910604509X

The program CHAINSAW (Schwarzenbacher et al. , 2004 ▶ ) was used to align the target sequence (YcdB) and the two model sequences from LiP (PDB code 1lga ) and MnP (PDB code 1mnp ) such that al... the atoms common to the three models were retained.

Publication Year: 2007


PocketMatch: a new algorithm to compare binding sites in protein structures.

(2008) BMC Bioinformatics 9

PubMed: 19091072 | PubMedCentral: PMC2639437 | DOI: 10.1186/1471-2105-9-543

For example, PyMol failed to align heme sites in Cytochrome c4 (1M6Z) and lignin peroxidase (1LGA), although PocketMatch found a significant similarity of more than 63% between them.

Publication Year: 2008


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

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 s... d3 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.

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 Average 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 .

Publication Year: 2009


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4364632

To design the second MnP6 variant, we compared the catalytic tryptophan surface environments in the P. ostreatus VP1 and P. chrysosporium LiP-H8 (1LGA) crystal structures (Figure  3 A and B), ... nd the corresponding region in the C. subvermispora MnP6 structure (Figure  3 D).

Publication Year: 2014