Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 4

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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Automated ligand fitting by core-fragment fitting and extension into density.

(2006) Acta Crystallogr D Biol Crystallogr 62

PubMed: 16855309 | PubMedCentral: PMC2745883 | DOI: 10.1107/S0907444906017161

( d ) Fit at 4.5 Å of 1-(4-iodobenzoyl)-5-methoxy-2-methyl-indole-3-acetic acid (PDB entry 1pgf ; Loll et al. , 1996 ▶ ).

Publication Year: 2006


On the use of logarithmic scales for analysis of diffraction data.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19966414 | PubMedCentral: PMC2789003 | DOI: 10.1107/S0907444909039638

R (mvd, set 5) ( R PDB ) ( R ) ( R free ) ( R free R ) 0.67 2vb1 2vb1   0.0911 0.1090 0.1175 0.0089 0.670.76 1yk4 1r6j 2pve 0.1035 0.1199 0.1317 0.0121 0.760.87 2ol9 2h5c 2h5c 0.1158 0.1307 0.... 459 0.0153 0.871.00 1ob7 1rb9 1ixb 0.1281 0.1416 0.1601 0.0185 1.001.14 1iro 1iro 1z3n 0.1405 0.1525 0.1742 0.0217 1.141.31 2v9l 1n0q 2v9l 0.1528 0.1634 0.1884 0.0250 1.311.50 1hbz 2plz 1hbz 0.1651 0.1743 0.2026 0.0282 1.501.72 2ah2 6rxn 2pfg 0.1775 0.1851 0.2168 0.0314 1.721.97 1amk 2dya 2dya 0.1898 0.1960 0.2310 0.0346 1.972.25 2oh5 2oh5 2oh5 0.2021 0.2069 0.2452 0.0378 2.252.58 2oh7 1uvw 1uvw 0.2145 0.2178 0.2594 0.0410 2.582.95 5bna 1tre 1f4h 0.2268 0.2286 0.2736 0.0443 2.953.37 1bgj 1sv2 1ydz 0.2391 0.2395 0.2878 0.0475 3.373.86 2d3b 1gn3 2q3n 0.2515 0.2504 0.3020 0.0507 3.864.42 1aos 1veq 1veq 0.2638 0.2613 0.3162 0.0539 4.425.06 2rkj 1pgf 2rkj 0.2761 0.2721 0.3304 0.0571 5.065.80 3b5w 2b66 3b5x 0.2885 0.2830 0.3445 0.0603 5.806.63 2b9n 2b9n 3e3j 0.3008 0.2939 0.3587 0.0635 6.637.59 3c4y 3c4y 1yv0 0.3131 0.3048 0.3729 0.0668 7.598.69 2dh1 2dh1 2dh1 0.3255 0.3157 0.3871 0.0700 8.699.95 1vcr 1zbb 1vcr 0.3378 0.3265 0.4013 0.0732

Publication Year: 2009


Super-resolution biomolecular crystallography with low-resolution data.

(2010) Nature 464

PubMed: 20376006 | PubMedCentral: PMC2859093 | DOI: 10.1038/nature08892

Table 2 DEN Refinement Improves Low Resolution Structures in the PDB a R free R free -R work Ramachandran Score PDB Identifier Resolution(Å) Number Residues DEN noDEN Improvement DEN noDEN DEN... noDEN Improvement Comments 1av1 4.00 804 0.335 0.336 0.0012 0.07 0.07 0.840 0.872 −0.0314 1isr 4.00 448 0.233 0.237 0.0043 0.07 0.07 0.833 0.833 0.0000 1jl4 4.30 557 0.353 0.354 0.0009 0.12 0.11 0.718 0.705 0.0127 1pgf 4.50 1102 0.284 0.295 0.0108 0.08 0.11 0.856 0.804 0.0519 Small differences throughout 1r5u 4.50 3517 0.334 0.335 0.0003 0.05 0.05 0.714 0.710 0.0046 1xdv 4.10 1517 0.358 0.367 0.0089 0.12 0.11 0.780 0.783 −0.0034 1xxi 4.10 3532 0.407 0.465 0.0582 0.05 0.12 0.842 0.612 0.2301 Large differences (~ 4 A domain motions) 1ye1 4.50 574 0.312 0.350 0.0381 0.08 0.15 0.894 0.705 0.1890 Small differences throughout 1yi5 4.20 1356 0.323 0.336 0.0139 0.07 0.09 0.758 0.709 0.0497 Local differences in several chains 1z9j 4.50 821 0.317 0.331 0.0135 0.07 0.09 0.838 0.762 0.0761 Large differences in chain A (domain motion) 2a62 4.50 319 0.340 0.353 0.0131 0.07 0.09 0.590 0.606 −0.0159 2bf1 4.00 304 0.479 0.492 0.0131 0.12 0.12 0.467 0.507 −0.0400 2i36 4.10 962 0.387 0.401 0.0137 0.02 0.03 0.839 0.687 0.1520 Local difference in chain B 2qag 4.00 702 0.392 0.401 0.0091 0.02 0.02 0.616 0.614 0.0016 2vkz 4.00 10941 0.327 0.337 0.0095 0.05 0.07 0.832 0.762 0.0692 Large differences in subdomain placements 3bbw 4.00 543 0.304 0.334 0.0304 0.01 0.04 0.876 0.776 0.0998 Significant local difference 3crw 4.00 485 0.324 0.338 0.0136 0.09 0.11 0.836 0.777 0.0589 Large difference in one domain (hinge motion) 3dmk 4.19 2127 0.407 0.428 0.0211 0.08 0.11 0.742 0.653 0.0896 Differences throughout, reference model only 50% 3du7 4.10 1839 0.332 0.336 0.0039 0.09 0.09 0.730 0.707 0.0225 Average 4.19 1708 0.345 0.359 0.0146 0.07 0.09 0.768 0.715 0.0535 Minimum 4.00 304 0.233 0.237 0.0003 0.01 0.02 0.467 0.507 −0.0400 Maximum 4.50 10941 0.479 0.492 0.0582 0.12 0.15 0.894 0.872 0.2301 a Nineteen PDB structures were re-refined with and without DEN ( Online Methods ).

Publication Year: 2010


Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.

(2012) Acta Crystallogr D Biol Crystallogr 68

PubMed: 22505258 | PubMedCentral: PMC3322597 | DOI: 10.1107/S0907444911047834

Both 1isr and 1pgf failed in reference torsion generation owing to significant bond-distance outliers in the reference-model file and were therefore excluded from this study.

Publication Year: 2012