Citations in PubMed

Primary Citation PubMed: 14709046 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

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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Combining specificity determining and conserved residues improves functional site prediction.

(2009) BMC Bioinformatics 10

PubMed: 19508719 | PubMedCentral: PMC2709924 | DOI: 10.1186/1471-2105-10-174

Table 1 Statistics of the benchmark datasets: diverse dataset, two or more EC numbers per family Family ID Family name # sequences Alignment length ECs PDB Bound ligand equivalent to natural substrate... product PF00108 Thiolase_N 22 291 2.3.1.9 2.3.1.16 2.3.1.176 1NL7 Coenzyme A PF00128 Alpha-amylase 54 673 2.4.1.4 2.4.1.7 3.2.1.10 3.2.1.20 3.2.1.70 3.2.1.98 3.2.1.93 3.2.1.141 5.4.99.16 5.4.99.15 2D3N Glucose PF00135 COesterase 129 889 3.1.1.1 3.1.1.3 3.1.1.7 3.1.1.8 3.1.1.13 3.1.1.59 1P0M Choline ion PF00215 OMPdecase 92 402 4.1.1.23 4.1.1.85 2CZE Uridine-5'-monophosphate PF00278 Orn_DAP_Arg_deC 55 220 4.1.1.17 4.1.1.18 4.1.1.19 4.1.1.20 1TWI Lysine PF00293 NUDIX 205 314 2.7.7.1 3.6.1.13 3.6.1.17 3.6.1.52 3.6.1.52 5.3.3.2 2DSC Adenosine-5-diphosphoribose PF00348 Polyprenyl_synt 16 289 2.5.1.10 2.5.1.29 2F8Z Zoledronic acid, 3-methylbut-3-enyl trihydrogen diphosphate PF00351 Biopterin_H 6 332 1.14.16.1 1.14.16.2 1.14.16.4 1MMK 5,6,7,8-tetrahydrobiopterin, beta(2-thienyl)alanine PF00579 tRNA-synt_1b 41 402 6.1.1.1 6.1.1.2 1WQ4 Tyrosine PF00583 Acetyltransf_1 244 150 2.3.1.1 2.3.1.4 2.3.1.48 2.3.1.57 2.3.1.59 2.3.1.82 2.3.1.87 2.3.1.88 2.3.1.128 1TIQ Coenzyme A PF00590 TP_methylase 22 247 2.1.1.98 2.1.1.107 2.1.1.130 2.1.1.131 2.1.1.132 2.1.1.133 2.1.1.152 2.1.1.151 4.2.1.75 4.99.1.4 1S4D S-adenosyl-L-homocysteine PF00755 Carn_acyltransf 22 867 2.3.1.6 2.3.1.7 2.3.1.21 2.3.1.137 1NDI Coenzyme A PF00871 Acetate_kinase 12 405 2.7.2.1 2.7.2.7 2.7.2.15 1TUY Adenosine-5'-diphosphate PF00896 Mtap_PNP 13 288 2.4.2.1 2.4.2.28 1V48 9-(5,5-difluoro-5-phosphonopentyl)guanine PF00962 A_deaminase 17 475 3.5.4.4 3.5.4.6 1NDZ 1-((1r)-1-(hydroxymethyl)-3-(6-((3-(1-methyl- 1h-benzimidazol-2-yl)propanoyl)amino)-1h- indol-1-yl)propyl)-1h-imidazole-4-carboxamide PF01048 PNP_UDP_1 16 276 2.4.2.1 2.4.2.3 2.4.2.28 3.2.2.4 3.2.2.9 1PK7 Adenosine PF01112 Asparaginase_2 7 365 3.5.1.1 3.5.1.26 1SEO Aspartic acid PF01135 PCMT 9 232 2.1.1.77 2.1.1.36 1R18 S-adenosyl-L-homocysteine PF01202 SKI 100 263 2.7.4.3 2.7.1.12 2.7.4.14 2.7.1.71 4.2.3.4 1WE2 Adenosine-5'-diphosphate PF01234 NNMT_PNMT_TEMT 7 289 2.1.1.1 2.1.1.28 2.1.1.49 2AN4 S-adenosyl-L-homocysteine PF01467 CTP_transf_2 66 302 2.7.7.1 2.7.7.3 2.7.7.14 2.7.7.15 2.7.7.18 2.7.7.39 1N1D [Cytidine-5'-phosphate] glycerylphosphoric acid ester PF01712 dNK 14 174 1.6.99.3 2.7.1.21 2.7.1.74 2.7.1.76 2.7.1.113 2.7.1.145 2A2Z Uridine-5'-diphosphate, 2'-deoxycytidine PF02274 Amidinotransf 32 455 2.1.4.1 3.5.3.6 3.5.3.18 2A9G Arginine PF03061 4HBT 153 102 3.1.2.2 3.1.2.23 1LO7 2-oxyglutaric acid, 2-aminoethanesulfonic acid PF03171 2OG-FeII_Oxy 147 183 1.14.11.2 1.14.11.4 1.14.11.7 1.14.11.9 1.14.11.11 1.14.11.13 1.14.11.19 1.14.11.20 1.14.11.23 1.14.11.26 1.14.17.4 1.14.20.1 1.21.3.1 2FDJ 4-hydroxyphenacyl coenzyme A PF03414 Glyco_transf_6 6 341 2.4.1.87 2.4.1.40 1LZJ Succinic acid Figure 1 Assessment of the prediction quality for the diverse dataset .

Publication Year: 2009


DINC: a new AutoDock-based protocol for docking large ligands.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24564952 | PubMedCentral: PMC3952135 | DOI: 10.1186/1472-6807-13-S1-S11

PDB ID 1NDZ This example represents a very challenging docking problem.

The structure of the complex deposited in the PDB with ID 1NDZ [ 48 ] contains a ligand with 10 rotatable bonds in complex with adenosine deaminase which is an enzyme that is found in almost all human tissues.

Figure 3 Docking example: PDB ID 1NDZ .

The conformation of the ligand from the structure of the complex deposited in the PDB (ID 1NDZ ) is shown in green color.

Publication Year: 2013