Cited Structures: list of articles citing SSGCID structures

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.

Cited structures

Structure	Year released	#citations
3T3W	2011	4
6BLJ	2017	4
4F3P	2012	4
4EYE	2012	4
4F4F	2012	4
4XK1	2015	4
4ECP	2012	4
3NJD	2010	4
4EG0	2012	4
6NAB	2019	4

Manually reviewed citations

#	PDB	Additional SSGCID structures cited	Link	Title	Year	Citation	Highlighted abstract
1	7lxw	7lxx, 7ly0, 7soa, 7sof, 7ly3	https://www.cell.com/cell-reports/pdf/S2211-1247(22)01868-X.pdf	Structural analysis of receptor engagement and antigenic drift within the BA. 2 spike protein	2023	JW Saville, D Mannar, X Zhu, AM Berezuk, S Cholak- Cell Reports, 2023 - cell.com	Cryo-EM structures of the BA.2 S-human ACE2 complex and of the extensively mutated BA.2 Our analysis reveals structural mechanisms underlying the antigenic drift in the rapidly
2	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.
3	4xk1	-	https://www.sciencedirect.com/science/article/pii/S014181301930755X	N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica	2019	RK Singh, P Tomar, S Dharawat, S Kumar- International journal of, 2019 - Elsevier	3. Comparative analysis, using the RAPIDO server, of PSAT structures from various organisms with the EhPSAT structure . PDB IDs, Sequence identity (%), RMSD with EhPSAT monomer in (number of residues compared) 4XK1 (P. aeruginosa) [38], 40, 1.52 (for 337 residues)
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	3nf4	-	https://www.sciencedirect.com/science/article/pii/S0021925820340461	Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate	2017	T Hino, H Hamamoto, H Suzuki, H Yagi- Journal of Biological, 2017 - Elsevier	2B). This domain architecture and quaternary structure are also seen for the acyl-CoA dehydrogenase superfamily (25), and the structure of TdsC is very similar to that of DszC (2122, 23 Structure of FMN-bound TdsC FMN binding to TdsC resulted in no global structural changes
6	6bfu	-	https://www.nature.com/articles/s41467-024-49693-0	Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein	2024	W Du, O Debski-Antoniak, D Drabek- Nature, 2024 - nature.com	the antigenic structure of the PDCoV S protein. Through functional and structural characterization The PDB file of PDCoV spike protein ( PDB ID: 6BFU ) and SARS-CoV-2 spike protein (
7	3k2h	-	http://www.sciencedirect.com/science/article/pii/S1368764615000540	Inside the biochemical pathways of thymidylate synthase perturbed by anticancer drugs: Novel strategies to overcome cancer chemoresistance	2015	L Taddia, D D'Arca, S Ferrari, C Marraccini - Drug Resistance , 2015 - Elsevier	The binding sites of other folate analogs (such as methotrexate) have been studied with TS isolated from other organisms (PDB IDs: 3K2H, 1AXW) and all share the same binding site..
8	6nb6	-	https://www.biorxiv.org/content/10.1101/2020.04.03.024885v1.abstract	Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing	2020	T Desautels, A Zemla, E Lau, M Franco, D Faissol- BioRxiv, 2020 - biorxiv.org	In the absence of a known SARS-CoV-2 spike protein structure , we characterized the SARS-CoV- 2 surface glycoprotein sequence YP_009724390.1 [13 The structures of the spike proteins from SARS-CoV-1 (Protein Data Bank ( PDB ) entries: 5x58 [15], 6nb6 [10], 2dd8 [11
9	4iuj	-	http://www.nature.com/nature/journal/v527/n7576/abs/nature15525.html	Crystal structure of the RNA-dependent RNA polymerase from influenza C virus	2015	N Hengrung, K El Omari, IS Martin, FT Vreede - Nature, 2015 - nature.com	... he published fragments of FluPolA (PDB accessions 4IUJ, 4AWH, 4CB4, 3A1G and 2VY7) were fitted by eye using Coot, which was used for all model building. ...
10	3obk	-	http://www.ingentaconnect.com/content/ben/ctmc/2013/00000013/00000001/art00006	Impact of quaternary structure dynamics on allosteric drug discovery	2013	EK Jaffe - Current topics in medicinal chemistry, 2013 - ingentaconnect.com	... Toxoplasma gondii PBGS (PDB id 3OBK, shown left) contains a 13 amino acid C-terminal exten- sion that forms a domain swapped beta sheet (orange/yellow), which locks the dimer into the pro-octamer conformation. Pseudomonas ...