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
3O2E	2010	9
3O0H	2010	9
5HA4	2016	9
3UF8	2011	9
3ECD	2008	9
3MQD	2010	9
3KRS	2009	9
2KHP	2009	9
3GRP	2009	9
3MX6	2010	9

Manually reviewed citations

#	PDB	Additional SSGCID structures cited	Link	Title	Year	Citation	Highlighted abstract
1	4f3y	4eqy, 5bq2, 5uy7	https://www.sciencedirect.com/science/article/pii/S0882401018312464	Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651	2018	Z Nazir, SG Afridi, M Shah, S Shams, A Khan- Microbial pathogenesis, 2018 - Elsevier	2.9. Protein 3D structures prediction. The target proteins structural information is vital for predicting immunogenic domains. The structure information of the target proteins was assessed by BLASTp analysis against Protein Data Bank ( PDB ) [42,43]. 2.10. Antigenicity prediction
2	3qh4	-	https://onlinelibrary.wiley.com/doi/abs/10.1002/ddr.21468	Microbial esterases and ester prodrugs: An unlikely marriage for combating antibiotic resistance	2018	EM Larsen, RJ Johnson- Drug development research, 2018 - Wiley Online Library	Bacterial esterase structure and function The bacterial esterase, LipW from M. tuberculosis ( PDB ID: 3QH4 ) is shown as an example with its sheets in tan, its helices in purple, and its catalytic triad in sticks and labeled
3	3oc6	3ico, 3v2i	https://www.mdpi.com/2073-4352/9/11/597	Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application	2019	C Oh, TD Kim, KK Kim- Crystals, 2019 - mdpi.com	In the Protein Data Bank ( PDB ), 136 crystal structures of bacterial CEHs (424 PDB codes) from The // sandwich architecture is most frequently found in CEHs, but 3-solenoid, are widely used in industrial applications, and are the objects of research in structure - or mutation ... 6-phosphogluconolactonases from M. smegmatis (representative PDB code: 3OC6) [140] belonging to group 3-4 CEHs contains His151-Glu149 as a catalytic dyad with nucleophilic water (Figure 3I).
4	8slg	-	https://www.nature.com/articles/s41467-024-48837-6	Structure prediction of protein-ligand complexes from sequence information with Umol	2024	P Bryant, A Kelkar, A Guljas, C Clementi- Nature, 2024 - nature.com	We parsed all protein sequences from the PDB files. 18884 out of 19119 protein structures (99%) could be parsed (<80% missing CAs and >50 residues). Only the first protein chain in
5	3uf8	-	https://www.mdpi.com/2076-3417/9/24/5389	Carotenoids Overproduction in Dunaliella Sp.: Transcriptional Changes and New Insights through Lycopene Cyclase Regulation	2019	F Elleuch, HB Hlima, M Barkallah, P Baril, S Abdelkafi- Applied Sciences, 2019 - mdpi.com	and cytochrome b 6 /f complex and maintains the integrity of cell architecture [7]. It attempted to understand how this stress could affect LCYB molecule by generating its 3D structure to 200 bp, chosen temperature (Tm) around 60 C, and avoiding secondary structures and self
6	5udf	-	https://www.sciencedirect.com/science/article/pii/S0959440X17301586	Translocation of lipoproteins to the surface of gram negative bacteria	2018	Y Hooda, TF Moraes- Current opinion in structural biology, 2018 - Elsevier	The model of LolCDE was obtained from the structure of LptBFG ( PDB ID: 5UDF )and is The structure of type IVa pilus machinery from Myxococcus xanthus ( PDB ID: 3JC9) was used as In contrast, Slam possesses a unique domain architecture and no structure of any protein of
7	3sbx	-	https://www.sciencedirect.com/science/article/pii/S1097276519302606	(p) ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch	2019	YE Zhang, RL Brentsen, T Fuhrer, U Sauer, K Gerdes- Molecular cell, 2019 - Elsevier	marinum showing similarity to the PpnN core domain and determined in the presence of adenosine monophosphate (AMP) ( PDB : 3SBX , Figure S3 Vibrio cholerae and Idomarina baltica, at a similar position to the phosphate of AMP in the M. marinum structure , suggesting that
8	4xwi	-	https://www.tandfonline.com/doi/abs/10.1080/07391102.2018.1459318	Towards novel inhibitors against KdsB: A highly specific and selective broad-spectrum bacterial enzyme	2018	S Ahmad, S Raza, A Abro, KR Liedl- Biomolecular Structure, 2018 - Taylor & Francis	from Protein Data Bank ( PDB ) with PDB ID, 4FCU (Berman et al., 2006). The protein is present (A. baumannii), 3K8D (E.coli), 4XWI (P. aeruginosa), 3TQD (C. Burnetii), 3QAM (V explicates enzyme structure stability and strong binding affinity of the compound towards the
9	5vwm	-	https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.9b01604	Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria	2019	JP Surivet, P Panchaud, JL Specklin- Journal of Medicinal, 2019 - ACS Publications	UDP-3-O-((R)-3-hydroxymyristoyl)-N-glucosamine deacetylase (LpxC) is as an attractive target for the discovery and development of novel antibacterial drugs to address the critical medical need crea...
10	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.