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
2KHR	2009	7
4WHX	2014	7
3HHJ	2009	7
4YWJ	2015	7
3IX6	2009	7
4H7P	2012	7
4O5H	2014	7
4EFI	2012	7
3I3F	2009	7
6VZZ	2020	7

Manually reviewed citations

#	PDB	Additional SSGCID structures cited	Link	Title	Year	Citation	Highlighted abstract
1	2lwk	-	https://www.sciencedirect.com/science/article/pii/S0168945218302693	RNA on the move: the plasmodesmata perspective	2018	BC Reagan, EE Ganusov, JC Fernandez, TN McCray- Plant Science, 2018 - Elsevier	While this synthetic RNA consists of only 32 nucleotides, it has a corresponding radius of gyration of 15.48 Å (1.548 nm) when bound to the small molecule DPQ (6,7-dimethoxy-2-(piperazin-1-yl)quinazolin-4-amine) (PDB ID: 2LWK)
2	3v7o	-	https://link.springer.com/article/10.1007/s00018-019-03303-1	Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription	2019	A Ivanov, P Ramanathan, C Parry, PA Ilinykh- Cellular and Molecular, 2019 - Springer	Three-dimensional structural models were built for NP, VP35, VP40, GP, VP30 and VP24 proteins using available crystal structures or by de novo structure prediction to elucidate the potential role of the phosphorylation sites
3	3ujh	-	https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.17368	Engineering of the cytosolic form of phosphoglucose isomerase into chloroplasts improves plant photosynthesis and biomass	2021	F Gao, H Zhang, W Zhang, N Wang, S Zhang- New, 2021 - Wiley Online Library	in Shanghai, China. Diffraction data were processed by HKL2000 and the PGIs structure models ( PDB : 3UJH ). After cycles of auto model building (PHENIX) (Liebschner et al., 2019) and To investigate the structural basis for the dramatic activity difference between TaPGIc and
4	3m4s	-	https://www.nature.com/articles/srep30494	Crystal structures of RidA, an important enzyme for the prevention of toxic side products	2016	X Liu, J Zeng, X Chen, W Xie- Scientific reports, 2016 - nature.com	2DYY, dirty violet), and Entamoeba histolytica l-PSP ( PDB code 3M4S , gray) respectively unpublished), and a putative endoribonuclease l-PSP from Entamoeba histolytica ( PDB code3M4S, unpublished AtRidA is highly similar to other RidA family members in structure , and their
5	7ry7	-	https://www.nature.com/articles/s41467-022-32271-7	Maturation and substrate processing topography of the Plasmodium falciparum invasion/egress protease plasmepsin X	2022	S Mukherjee, S Nguyen, E Sharma- Nature, 2022 - nature.com	The crystal structure of PM X that was used in this study is deposited in the protein data base ( PDB ) under PDB ID: 7RY7 . The mass spectrometry proteomics data have been deposited
6	5vwm	-	https://www.sciencedirect.com/science/article/pii/S0968089620306568	N-Hydroxyformamide LpxC inhibitors, their in vivo efficacy in a mouse Escherichia coli infection model, and their safety in a rat hemodynamic assay	2020	T Furuya, AB Shapiro, J Comita-Prevoir- Bioorganic & Medicinal, 2020 - Elsevier	Fig. 2. Key interactions in the LpxC enzyme binding pocket observed in P. aeruginosa LpxCCHIR-090 (3) co-crystal structure ( PDB code: 5VWM ). We first implemented a docking model using the ICM-Pro software (Molsoft) based on the available co-crystal structures of P
7	4zju	-	https://www.sciencedirect.com/science/article/pii/S0968089617318217	A Novel Series of Enoyl Reductase Inhibitors Targeting the ESKAPE Pathogens, Staphylococcus aureus and Acinetobacter baumannii	2017	J Kwon, T Mistry, J Ren, ME Johnson- Bioorganic & Medicinal, 2017 - Elsevier	and AbFabI. These enzymes share a high sequence identity (45% identity) and structural similarity (RMSD for all residues < 1 when the various crystal structures of SaFabI are overlaid with the crystal structure of AbFabI). As a
8	3ix6	-	https://www.nature.com/articles/s41598-019-48940-5	Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis	2019	B Pandey, S Grover, J Kaur, A Grover- Scientific reports, 2019 - nature.com	crystal structures of the ThyA enzyme in Brucella melitensis (PDBID: 3IX6 ), M. tuberculosis 3QJ7) 20 , Enterococcus faecalis ( PDB IF: 6QYA), and Escherichia coli ( PDB ID: 1AXW Comparative analysis of the binding free energy, secondary structure elements, and free energy
9	3hhj	-	http://www.jbc.org/content/285/1/444.short	Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base	2010	T Nakamura, S Meshitsuka, S Kitagawa, N Abe? - Journal of Biological Chemistry, 2010 - ASBMB	... ?, Z = 19.0) and with dGTP (BdRppH-dGTP, 3EF5, rmsd = 1.9 ?, Z = 18.3) (40) and unknown proteins from Bartonella henselae (3HHJ, rmsd = 1.8 ... ray and NMR structures in the ligand-free form and 3.5 ?for 127 C? atoms between structures in the complex form (PDB IDs: 1MUT ...
10	6nb7	-	https://www.nature.com/articles/s41598-020-73820-8	Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital	2020	H Lim, A Baek, J Kim, MS Kim, J Liu, KY Nam- Scientific reports, 2020 - nature.com	the hot spot region, we also performed the same calculation with RBD-SARS-CoV-1/antibody complexes (five experimental structural data All experimental structures calculated in this work are summarized in Table 1. All missing side chains were filled using Prime implemented