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
6CKG	2018	0
6CKP	2018	0
6CU3	2018	0
6CXM	2018	0
6CY5	2018	0
6EEP	2018	0
6EFW	2018	0
6EFX	2018	0
6MDY	2018	0
6MFU	2018	0

Manually reviewed citations

#	PDB	Additional SSGCID structures cited	Link	Title	Year	Citation	Highlighted abstract
1	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
2	4wgj	-	https://www.biorxiv.org/content/10.1101/2020.04.17.046482v1.abstract	Bartonella effector protein C mediates actin stress fiber formation via recruitment of GEF-H1 to the plasma membrane	2020	S Marlaire, C Dehio- BioRxiv, 2020 - biorxiv.org	On the 130 structural level, BepC displays the ancestral FIC-OB-BID architecture . However, 131 replacement of an acidic residue (D/E) by a lysine (K). The crystal structure of the 134 the - and -phosphates of the ATP analog ( PDB : 4WGJ ), thus functionally replacing 137
3	6q05	-	https://www.biorxiv.org/content/10.1101/2020.04.17.047548v1.abstract	Distinct structural flexibility within SARS-CoV-2 spike protein reveals potential therapeutic targets	2020	SH Chen, MT Young, J Gounley, C Stanley, D Bhowmik- BioRxiv, 2020 - biorxiv.org	of SARS-CoV-2 ( PDB 6VSB [3]), SARS-CoV-1 ( PDB 6CRZ [15]), MERS- CoV ( PDB 6Q05 [16]), and The trimeric state of the SARS-CoV-2 S protein consists of all three chains in PDB 6VSB Each structure was solvated in the center of a water box with a minimum distance of 15 A
4	6c9e	-	https://www.biorxiv.org/content/10.1101/2020.05.24.113720v1.abstract	Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism	2020	RJ Nichols, B LaFrance, NR Phillips, LM Oltrogge- bioRxiv, 2020 - biorxiv.org	additional density for the holo-SrpI with a 243 homologous cysteine desulfurase dimer docked in ( pdb : 6c9e ) the first Family 2 encapsulin structure and is 267 the highest resolution structure for an Given the structural 271 similarity of the entire shell, it is unsurprising that the SrpI
5	3tcq	-	https://www.biorxiv.org/content/10.1101/2020.05.27.108969v1.abstract	Common substructures and sequence characteristics of sandwich-like proteins from 42 different folds	2020	A Kister- BioRxiv, 2020 - biorxiv.org	structural classification in PDBSum database30 does not support sandwich-like architecture was examined. For secondary structure analysis, the information about localization of strands in sequences was taken from PDB .31 For supersecondary structure (SSS) of the domains
6	3tjr	-	https://www.biorxiv.org/content/10.1101/2020.07.15.204123v2.abstract	On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment	2020	LM Longo, J Jablonska, P Vyas, R Kolodny, N Ben-Tal- bioRxiv, 2020 - biorxiv.org	between Rossmanns and P-loops, ideally with respect to not only structure but also sequence 2003.1.1.417; PDB : 1k2w) and short chain dehydrogenase (F-Group 2003.1.1.332; PDB : 3tjr ) showing the highest overlap (Figure 4)
7	3eiy	-	https://www.biorxiv.org/content/10.1101/2020.07.15.204701v1.abstract	Graphein-a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures	2020	AR Jamasb, P Li, T Blundell- bioRxiv, 2020 - biorxiv.org	Figure 1. Example outputs from Graphein. A Example protein surface ( 3eiy ). B Example node feature matrix for the residue-level graphs outlined The interaction status data and structure originate from structures of the complexes in the RCSB PDB
8	6bfu	6q04, 6nb3, 6q05, 6q07, 6nb4, 6nb7, 6q06	https://www.biorxiv.org/content/10.1101/2020.07.16.207308v3.abstract	Systematic modeling of SARS-CoV-2 protein structures	2020	SI O'Donoghue, A Schafferhans, N Sikta, C Stolte- bioRxiv, 2020 - biorxiv.org	CoV, 82% identity, E = 10-24) with a fold not seen in any other PDB structure (CATH 3.40 from SARS-CoV-2, 98% identity, E = 10-44), all with beta barrel architecture (CATH 2.40 6acg from SARS-CoV, 77% identity, E = 10-321), of which one structure also showed
9	3sdo	-	https://www.biorxiv.org/content/10.1101/2020.08.24.261826v1.abstract	On the diversity of F420-dependent oxidoreductases: a sequence-and structure-based classification	2020	ML Mascotti, MJ Ayub, M Fraaije- bioRxiv, 2020 - biorxiv.org	monooxygenase (NTA_MO, PDB : 3sdo ), as well as the well-known bacterial FMN- dependent luciferases (eg.: LuxB, PDB : 1luc) [28]. The topology suggests that cofactor vary considerably in structure and function, and comprise the F420H2-NADP+ oxidoreductases
10	3vab	-	https://www.biorxiv.org/content/10.1101/2020.10.01.322594v1.full-text	The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate	2020	VA Bielinski, JK Brunson, A Ghosh, MA Moosburner- bioRxiv, 2020 - biorxiv.org	in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA. ... Akin to protomer 2 of PtLYSA, this segment is not included in the structures of DAPDC from Aquifex aeolicus (PDB 2P3E) and Brucella melitensis (PDB 3VAB).