We are actively tracking the number of publications by the scientific community which reference our structures, whether in the main text, figure captions or supplementary material. Selected articles are manually reviewed. Publications by SSGCID authors are excluded from the manually reviewed list. From our manual curation results, we estimate that the false positive rate might be as high as 50% for some structures.
This list was obtained from Google Scholar searches using an API provided by Christian Kreibich.
| Structure | Year released | #citations |
|---|---|---|
| 6TYS | 2020 | 18 |
| 3EOO | 2008 | 17 |
| 3IJP | 2009 | 17 |
| 3SDO | 2011 | 16 |
| 6BFU | 2017 | 16 |
| 3RD5 | 2011 | 15 |
| 7LY2 | 2021 | 15 |
| 4IX8 | 2014 | 15 |
| 3R20 | 2011 | 14 |
| 3D64 | 2008 | 14 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3meq | - | https://www.frontiersin.org/articles/10.3389/fmicb.2017.00944 | Adaptations to high salt in a halophilic protist: differential expression and gene acquisitions through duplications and gene transfers | 2017 | T Harding, AJ Roger, AGB Simpson- Frontiers in microbiology, 2017 - frontiersin.org | WP_041596283.1), and sequences for characterized NADPH-dependent enzymes from S. cerevisiae (1Q1N), P. perezi (1P0C), Helicobacter pylori (3TWO), Populus tremuloides (1YQD) and Catharanthus roseus (5H81), and for NADH-dependent enzymes from Moraxella sp. (4Z6K), Geobacillus stearothermophilus (3PII), Ralstonia eutropha (3S1L), Brucella suis (3MEQ), and Pseudomonas aeruginosa (1LLU). (B) Maximum-likelihood phylogenetic tree for zinc-dependent alcohol dehydrogenase showing strongly supported clustering (gray |
| 2 | 4kam | - | https://www.nature.com/articles/s42003-020-0954-9 | Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum | 2020 | Y Wang, L Fan, P Tuyishime, J Liu, K Zhang- Communications, 2020 - nature.com | Synthetic methylotrophy has recently been intensively studied to achieve methanol-based biomanufacturing of fuels and chemicals. However, attempts to engineer platform microorganisms to utilize methanol mainly focus on enzyme and pathway engineering... The model structure of the wild-type Cgl0653 was constructed with the crystal structure of O-acetyl-L-homoserine sulfhydrylase from Mycobacterium marinum ATCC BAA-535 (PDB ID: 4KAM) as a template (54% sequence identity with Cgl0653) |
| 3 | 2kok | - | https://royalsocietypublishing.org/doi/abs/10.1098/rsfs.2019.0003 | A deep learning approach to the structural analysis of proteins | 2019 | M Giulini, R Potestio- Interface focus, 2019 - royalsocietypublishing.org | Second, we show that the application of a simple, standard and computationally not expensive DL architecture to the selected features gives satisfactory results, suggesting that The raw data employed in the present work, including PDB files, protein structure datasets, CNN ... Eigenvalues associated with 2KOK, 2YQD, and 1MEK were predicted with reasonable accuracy, the overall average MAPE being 30.7, 35.5 and 48.3, respectively. |
| 4 | 3gmt | - | http://www.sciencedirect.com/science/article/pii/S2211546314000679 | Adenylate kinase from< i> Streptococcus pneumoniae</i> is essential for growth through its catalytic activity | 2014 | TT Thach, TT Luong, S Lee, DK Rhee - FEBS Open Bio, 2014 - Elsevier | ... Open, ligand-free SpAdK structure was solved by molecular replacement using PHENIX [35] with AdK from Marinibacillus marinus (PDB ID: 3FB4) and Burkholderia pseudomallei (PDB ID: 3GMT) as search models. ... |
| 5 | 3laa | - | http://www.sciencedirect.com/science/article/pii/S1438422114001696 | A domain dictionary of trimeric autotransporter adhesins | 2014 | J Bassler, BH Alvarez, MD Hartmann… - International Journal of …, 2014 - Elsevier | ... Name, Description, Topological crossover, PDB. Anchor, Trimeric, 12-stranded outermembrane β-barrel, –, 2gr7. Stalk, Slender segment of predominantly coiled-coil structure, –, ...Long neck, Neck variant of 22 residues length, 120° cw, 3laa. ... |
| 6 | 6b4a | - | https://www.biorxiv.org/content/10.1101/623140v1.abstract | A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers | 2019 | JM Leung, E Nagayasu, YC Hwang, P Pierce, IQ Phan- bioRxiv, 2019 - biorxiv.org | Page 5. 5 more in-depth analysis of the conoid fiber architecture , and a comparison of TgDCX and its eight residues 51-128, rmsd 1.905 ); TgDCX ( 6B4A , chain A, aa150-222) vs DCX domains (Figure 5A, Table 1), we used the structure of TgDCX148-243 as a model for |
| 7 | 4di0 | - | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114695/ | Aerobic lineage of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic,(hyper) thermophilic environment | 2016 | JP Cardenas, R Quatrini, DS Holmes - Frontiers in Microbiology, 2016 - ncbi.nlm.nih.gov | ... F9VPE5; PDB entry 1J30) and a rubrerythrin from Burkholderia pseudomallei (Uniprot accessionQ3JK2; PDB entry 4DI0) have three dimensional structures in the PDB. ... This difference in genecluster structure among members of the same phylum may be a reflection of the ... |
| 8 | 3s4k | - | http://onlinelibrary.wiley.com/doi/10.1002/prot.25282/full | A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism | 2017 | A SnchezReyez, RA BatistaGarca - Proteins: Structure, , 2017 - Wiley Online Library | ... All other parameters were set as default unless otherwise noted. Structure modelling by homology. ...In our first attempt to model ThYest_ar, I-TASSER[31] selected as templates from the PDB bacterial thioesterases (validated and putative): 1VH9 and 1VH5 (putative thioesterases from E. coli), 4K4C (thioesterase from E. coli), 1Q4T (thioesterase from Arthrobacter), 1SH8 (putative thioesterase from P. aeruginosa), 1SC0 (putative thioesterase from Haemophillus influenzae), 3S4K (putative esterase from ... |
| 9 | 3ek2 | - | http://onlinelibrary.wiley.com/doi/10.1002/pro.2655/abstract | AFN‐1252 is a potent inhibitor of Enoyl‐ACP reductase from Burkholderia pseudomallei‐Crystal structure, Mode of action and biological activity | 2015 | KN Rao, A Lakshminarasimhan, S Joseph… - Protein …, 2015 - Wiley Online Library | ... due to poor electron density. The structural models were generated using Pymol. 34 Summaryof ... The overall structure of BpmFabI in complex with AFN-1252 is similar to the earlier reportedapo-structure of Bpm FabI (PDB:3EK2) and ternary complex structures of Ec (E. coli: ... |
| 10 | 4o5o | - | https://academic.oup.com/peds/article-abstract/doi/10.1093/protein/gzab008/62691... | A fragment-based protein interface design algorithm for symmetric assemblies | 2021 | J Laniado, K Meador, TO Yeates- Protein Engineering, Design, 2021 - academic.oup.com | The expansive database of known protein structures provides valuable empirical frameworks for The growing focus on secondary structure associations motivates an attempt to bring by precomputing common proteinprotein fragment configurations from known structural data |