Citations in PubMed

Primary Citation PubMed: 15299316 Citations in PubMed

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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Entropic stabilization of proteins and its proteomic consequences.

(2005) PLoS Comput Biol 1

PubMed: 16201009 | PubMedCentral: PMC1239905 | DOI: 10.1371/journal.pcbi.0010047

Accession Numbers The Protein Data Bank ( http://www.rcsb.org/pdb/ ) accession numbers for products used in this paper are 2Fe-2S ferredoxin (4FXC, 1FRR, 1FRD, 1DOI, and 2CJN); 4Fe-4S ferredoxin (1FCA... 1DUR, 1IQZ, and 1VJW); chemotaxis protein (3CHY, 2CHF, and 1TMY); Cytochrome C (1DW0); hydrolases (1INO [from E. coli ] and 2PRD [from T. thermophilus ]); rubredoxins (1RDG, 5RXN, 8RXN, and 1CAA).

Publication Year: 2005


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. lattice_ssfit 1beo 1/1998 0.0 -5.6 0.08 12.6 lattice_ssfit 1ctf 1/2001 0.0 -6.0 0.03 16.0 lattice_ssfit 1dkt-A 1/1999 0.0 -3.1 -0.01 11.6 lattice_ssfit 1fca 1/2001 0.0... -4.7 0.04 9.0 lattice_ssfit 1nkl 1/1998 0.0 -4.1 0.01 14.1 lattice_ssfit 1pgb 1/2000 0.0 -4.7 0.04 10.5 lattice_ssfit 1trl-A 1/2000 0.0 -3.6 0.02 10.0 lattice_ssfit 4icb 1/2000 0.0 -4.4 -0.00 15.5 Table 8 Performance evaluation of the energy function on lmds decoy set Decoy set PDB id.

Publication Year: 2007


OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

(2003) BMC Bioinformatics 4

PubMed: 14552658 | PubMedCentral: PMC280650 | DOI: 10.1186/1471-2105-4-47

Inspection of the structure superposition in this region shows that despite its position in the sequence, the proline at position 24 in 2fxb is not structurally equivalent to the prolines in 1fdn and ... fca, while the valine at position 24 in 1fdn and 1fca should be shown as an insertion.

Publication Year: 2003


Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions.

(2010) BMC Bioinformatics 11

PubMed: 20624289 | PubMedCentral: PMC2912888 | DOI: 10.1186/1471-2105-11-374

1 7.1 1200 8.5 - 17.0  1bg8-A 2.20 1 6.1 1200 6.0 - 15.8  1bl0 2.30 1 6.0 972 3.6 - 18.2  1eh2 NMR 1 4.4 2413 4.0 - 15.3  1jwe NMR 1 8.3 1407 7.8 - 20.9 lattice_ssfit &... x02003;4icb 1.60 1 5.1 1988 4.7 - 12.9  1ctf 1.70 1 6.2 1999 5.4 - 12.8  1fca 1.80 1 4.2 1986 5.1 - 11.4  1pgb 1.92 1 6.2 1997 5.8 - 12.9  1beo 2.20 1 6.6 1998 7.0 - 15.6  1dkt-A 2.90 1 5.5 1995 6.7 - 14.0  1nkl NMR 1 5.2 1995 5.3 - 13.6  1trl-A NMR 1 5.8 1998 5.4 - 12.5 lmds  1igd 1.10 1 8.1 501 3.1 - 12.6  2ovo 1.50 1 5.6 348 4.4 - 13.4  4pti 1.50 1 5.2 344 4.9 - 13.2  1ctf 1.70 1 7.6 496 3.6 - 12.5  1b0n-B 1.90 1 5.3 498 2.4 - 6.0  1shf-A 1.90 1 7.7 437 4.4 - 12.3  2cro 2.35 1 7.7 501 3.9 - 13.5  1fc2 2.80 49 1.5 501 4.0 - 8.4  1bba NMR 501 -3.8 501 2.8 - 8.9  1dtk NMR 3 3.6 216 4.3 - 12.6 Each decoy structure and the native structure were scored and ranked using the Hunter's ScSc term only.

Publication Year: 2010


BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements.

(2012) PLoS One 7

PubMed: 23173051 | PubMedCentral: PMC3500277 | DOI: 10.1371/journal.pone.0049242

set Pdb-Chain DFIRE R osetta ModPipe-Pair ModPipe-Surf ModPipe-Comb DOPE BCL::Score fisa 1fc2 254 158 491 1 453 375 480 fisa 1hdd-C 1 90 293 18 135 1 60 fisa 2cro 1 26 11 146 19 1 1 fisa 4icb 1 1 196 ... 167 1 1 correct 3 1 0 1 (2) 0 3 2 fisa_casp3 1bg8-A 1 1068 1 1180 282 1 9 fisa_casp3 1bl0 1 960 4 912 86 1 246 fisa_casp3 1jwe 1 1177 1 1119 6 1 1 correct 3 0 2 (3) 0 0 (1) 3 1 (2) lmds 1b0n-B 430 300 56 186 18 34 182 lmds 1bba 501 174 501 117 444 501 469 lmds 1fc2 501 291 325 54 222 476 501 lmds 1ctf 1 1 1 1 1 1 12 lmds 1dtk 1 9 4 1 1 1 4 lmds 1igd 1 1 1 3 1 1 1 lmds 1shf-A 1 5 24 18 7 1 2 lmds 2cro 1 2 4 28 12 1 1 lmds 2ovo 1 29 5 8 2 1 1 lmds 4pti 1 4 1 44 1 1 3 correct 7 2 (6) 3 (6) 2 (4) 4 (6) 7 3 (6) lattice_ssfit 1beo 1 1 1 1 1 1 1 lattice_ssfit 1ctf 1 1 1 1 1 1 1 lattice_ssfit 1dtk-A 1 1 1 35 1 1 1 lattice_ssfit 1fca 1 1 1 4 1 1 1 lattice_ssfit 1nkl 1 1 1 1 1 1 1 lattice_ssfit 1pgb 1 1 1 3 1 1 1 lattice_ssfit 1trl-A 1 45 1 123 1 1 6 lattice_ssfit 4icb 1 1 1 3 1 1 1 correct 8 7 8 3 (6) 8 8 7 (8) sum rank 1 21 10 13 6 12 21 13 sum rank 10 21 14 17 12 15 21 18 For different model sets from “decoys‘r’us” [39] , the rank of the native structure, using different energy potentials, was determined.

Publication Year: 2012