Citations in PubMed

Primary Citation PubMed: 8805555 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

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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Predicting functional sites with an automated algorithm suitable for heterogeneous datasets.

(2005) BMC Bioinformatics 6

PubMed: 15890082 | PubMedCentral: PMC1142304 | DOI: 10.1186/1471-2105-6-116

Table 3 Structural assessment of the phylogenetic motif functional site predictions a Protein family PDB ID Correct Useful info Wrong A. Proteins from Table 1 Acetyglucosamine-6-phoshate deacyetylase ... 1O12 6 1 0 Alcohol dehydrogenase 1JVB 2 1 1 CuZnSOD 1SPD 3 2 1 Cytochrome P450 1N4G 6 4 0 Enolase 2ONE 6 2 0 Glyceroladhyde-3-phosphate dehydrogenase 1DC4 2 2 3 Glycerol kinase 1B05 7 1 0 Glutamate dehydrogenase 1HWZ 7 0 0 Inorganic pyrophosphatase 1I6T 3 2 0 Myoglobin 1MBA 4 1 0 Succinate dehydrogenase – FAD 1NEK 4 1 2 Succinate dehydrogenase – Fe/S 1NEK 4 0 0 Succinate dehydrogenase – Heme 1NEK 5 0 0 TATA box binding protein 1TBP n/a c Triosephosphate isomerase 7TIM 3 4 1 B. Additional examples Acetate kinase 1G99 4 4 0 Aconitase A 7ACN 8 3 5 Alanine racemase 1L6F 4 1 1 Arginyl-tRNA synthetase 1F7U 2 2 1 Biotin carboxylase b 1DV2 3 3 2 Catalase 1GGF 9 0 0 Citrate synthase 1NXG 8 1 0 Isocitrate dehydrogenases 1IA2 3 0 0 Malate/lactate dehydrogenases 1EMD 6 1 0 Malate synthase 1P7T 6 0 0 Phosphomannomutase 1P5D 5 2 0 Selenocysteine lyase 1ECX 5 2 1 Threonine aldolase 1LW5 6 2 0 Thymidylate synthase 1AIQ 4 0 1 Transaldolase 1ONR 1 1 1 Trehalose-6-phosphate synthase 1UQU 5 3 3 a A sequence window width of 5 is used for each of the above examples and gap range of {-1: -2}.

Publication Year: 2005


A comprehensive analysis of non-sequential alignments between all protein structures.

(2007) BMC Struct Biol 7

PubMed: 18005453 | PubMedCentral: PMC2213659 | DOI: 10.1186/1472-6807-7-78

Consider as an example, the structure alignment of transaldolase B from Escherichia coli (PDB-code 1onr :A) and class I aldolase from Drosophila melanogaster (PDB-code 1fba :A) shown in Figure 9 .

Structures of transaldolase B (PDB-code 1onr :A) and class I aldolase (PDB-code 1fba :A) have been aligned by TOPOFIT with Ne/RMSD of 142/1.8 Å.

Publication Year: 2007