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 |
|---|---|---|
| 4G5D | 2012 | 16 |
| 3TCQ | 2012 | 16 |
| 3SWO | 2011 | 16 |
| 7LY2 | 2021 | 15 |
| 5DVW | 2015 | 15 |
| 3RD5 | 2011 | 15 |
| 3MEQ | 2010 | 15 |
| 3P0X | 2010 | 15 |
| 6NB8 | 2019 | 15 |
| 3GWC | 2009 | 14 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 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. ... |
| 2 | 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 |
| 3 | 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 ... |
| 4 | 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 |
| 5 | 5cy4 | - | https://munin.uit.no/handle/10037/17279 | A functional and structural study of three bacterial nucleic acid-interacting proteins. The story of a Ferric Uptake Regulator, an Oligoribonuclease and an ATP | 2020 | K Berg - 2020 - munin.uit.no | Acinetobacter baumannii (PDB 5CY4) and E. coli (PDB code 1YTA )[148]. All Orn homologs are structurally similar and topologically arranged |
| 6 | 5thw | 4wjb, 5i4m | https://www.nature.com/articles/s41598-018-31259-y | A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase | 2018 | T Sommer, K Bjerregaard-Andersen, L Uribe- Scientific reports, 2018 - nature.com | with a central scaffold resembling the swivelling // fold 18 , while the majority of AHS members contains a monomeric (/) 8 -TIM like-barrel structural fold 19 The finalised model and structure factors were deposited to Protein Data Bank ( PDB ) and given the PDB |
| 7 | 2lgo | - | https://www.biorxiv.org/content/10.1101/431635v1.abstract | A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures | 2018 | J Zhou, AE Panaitiu, G Grigoryan- bioRxiv, 2018 - biorxiv.org | decompose the target structure to be designed into structural building blocks we call TERMs (tertiary motifs) and use rapid structure search against the Protein Data Bank ( PDB ) to identify sequence patterns associated with each TERM from known protein structures that contain it |
| 8 | 3sbx | - | https://www.nature.com/articles/s41598-017-12471-8 | A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis | 2017 | R Bhagavat, HB Kim, CY Kim, TC Terwilliger- Scientific reports, 2017 - nature.com | a given ligand recognition, and (d) sensitive methods are required to compare structural motifs against binding sites 33 and combine them into a workflow to obtain structure -based function a large-scale analysis of 4,766 ATP and other NTP binding proteins from PDB and have |
| 9 | 3hhe | - | http://jb.asm.org/content/195/9/2101.short | A genomic signature and the identification of new sporulation genes | 2013 | AB Abecasis, M Serrano, R Alves, L Quintais… - Journal of Bacteriology, 2013 - Am Soc Microbiol | Supplemental Material: B: structure based alignment between the YlzA protein and a putative ribose-5-phosphate isomerase from Bartonella henselae (pdb code 3HHE). Note that that the first 20 residues of YlzA do not align with the B. henselae protein. |
| 10 | 4gnv | - | https://pubs.rsc.org/en/content/articlehtml/2018/cc/c8cc05281f | A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to -lactams in Pseudomonas | 2018 | LA Ho, JL Winogrodzki, AW Debowski- Chemical, 2018 - pubs.rsc.org | Fig. 2 Crystal structure of BcNagZ bound to 2. (A) Electron density (sigma-A weighted difference map (mF o DF c ) contoured at 4) for 2 (green carbon atoms (B) BcNagZ active site bound to 2 (green carbon atoms) with the BcNagZ product complex PDB 4GNV superposed |