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
6XK2	2020	0
6XNQ	2020	0
6XR5	2020	0
5F9Y	2016	0
7JFN	2020	0
5I92	2016	0
4XFK	2015	0
3O0K	2010	0
6D46	2018	0
4XGH	2015	0

Manually reviewed citations

#	PDB	Additional SSGCID structures cited	Link	Title	Year	Citation	Highlighted abstract
1	3ixc	-	https://www.frontiersin.org/articles/10.3389/fmicb.2020.00742/full?report=reader	Crystal structure and active site engineering of a halophilic -carbonic anhydrase	2020	M Vogler, R Karan, D Renn, A Vancea- Frontiers in, 2020 - frontiersin.org	(C) The surface potential of CA_D compared to mesophilic -CA homologs (Escherichia coli, 3tio; Salmonella enterica, 3r3r; Anaplasma phagocytophilum, 3ixc ; Bacillus cereus, 1xhd (A) CA_D (crystal structure ), (B) Cam (crystal structure ) from M. thermophila ( PDB ID: 1qrg
2	3gbz	-	https://pubs.rsc.org/--/content/articlehtml/2020/me/c9me00097f	How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family	2020	Z Shamsi, D Shukla- Molecular Systems Design & Engineering, 2020 - pubs.rsc.org	PDB ID: 5OSM, 6Q3F, 6Q4A, 6Q4B, 6Q4C, 6Q4D, 6Q4K), G/CDK ( PDB ID: 3GBZ ), and pfpk5 on the GA341 score and have comparable DOPE scores with the CDK2 native structure as shown Template's PDB ID, DOPE score for CMGI, DOPE score for native CDK2, GA341 score
3	6ar7	-	https://www.mlsb.io/papers/MLSB2020_Learning_Super-Resolution_Electron_Density.p...	Learning Super-Resolution Electron Density Map of Proteins using 3D U-Net	2020	B Mullick, Y Wang, P Yadav, AB Farimani - mlsb.io	The mesh grid displays the electron density surface for the structure and the underlying line diagram represents the protein structure from the PDB file. (a) The electron density map of PDB ID: 6AR7 (Green), with resolution of 2.10
4	6vxx	-	https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.0c04553	Developing a fully glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane	2020	H Woo, SJ Park, YK Choi, T Park- The Journal of, 2020 - ACS Publications	This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-l...
5	6vxx	-	https://www.nature.com/articles/s41392-020-00392-4	Bimodular effects of D614G mutation on the spike glycoprotein of SARS-CoV-2 enhance protein processing, membrane fusion, and viral infectivity	2020	X Jiang, Z Zhang, C Wang, H Ren, L Gao- Signal transduction and, 2020 - nature.com	structure of S glycoprotein, we performed three-dimensional (3D) modeling with the template of published SARS-CoV-2 S structure ( 6vxx . pdb ) by the idea that the D614G mutation may affect the stability of the S protein trimer as suggested above based on structural analysis (Fig
6	6vxx	-	https://pubs.acs.org/doi/abs/10.1021/acsmedchemlett.0c00410	Structural impact of mutation D614G in SARS-CoV-2 spike protein: enhanced infectivity and therapeutic opportunity	2020	A Fernndez- ACS medicinal chemistry letters, 2020 - ACS Publications	Figure 1. Structural and epistructural interactions at the S1/S2 interface in the spike protein of SARS-CoV-2. (a) Positioning of D614 in the S1 chain (magenta) relative to T859 in the S2 chain (blue) at the S1/S2 interface for the spike protein structure reported in PDB6VXX
7	2kn9	-	https://www.biorxiv.org/content/10.1101/2020.10.27.356691v1.abstract	A new twist of rubredoxin function in M. tuberculosis	2020	T Sushko, A Kavaleuski, I Grabovec, A Kavaleuskaya- bioRxiv, 2020 - biorxiv.org	21]. Previously, a zinc-substituted RubB structure was solved by NMR ( PDB ID: 2KN9 ). Pairwise . In the NMR model, residues at C and N termini show backbone variability, while the rest of the structure remain almost unperturbed
8	3s6d	-	https://www.biorxiv.org/content/10.1101/2020.12.04.412312v2.abstract	Leptospira interrogans triosephosphate isomerase: exploring the structural determinants of stability, high reaction rate and specificity.	2020	V Pareek, V Dhayabarn, H Balaram, PR Krishnaswamy- bioRxiv, 2020 - biorxiv.org	Contrary to our observation for the LiTIM structure , the backbone -CO of Trp11 has previously been observed in other TIMs (eg Page 15. 15 rare example of Glu at position 94 (LiTIM numbering) is in Coccidiodes immitis ( PDB ID: 3S6D ; Figures S2 and S5B)
9	6vyb	-	https://link.springer.com/article/10.1007/s11224-020-01586-w	Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination	2020	SA Ahmed, DA Abdelrheem, HR Abd El-Mageed- Structural Chemistry, 2020 - Springer	Protein preparation. The 3D crystal structure of the SARS-CoV-2 main protease Mpro ( PDB ID: 6LU7) and the cryo-electron microscopic structure of the SARS-CoV-2 spike protein Sp ( PDB ID: 6VYB ) were taken from the PDB (Protein Data Bank) site
10	5ucm	-	https://www.sciencedirect.com/science/article/pii/S002192581750441X	Human trans-editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity	2020	O Vargas-Rodriguez, M Bakhtina, D McGowan- Journal of Biological, 2020 - Elsevier	Corrections to the resulting alignment were made based on the structural alignment of Cc ProXp-ala (Protein Data Bank entry 5VXB) and Pa ProRS (Protein Data Bank entry 5UCM).