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.
| Structure | Year released | #citations |
|---|---|---|
| 8T1A | 2023 | 0 |
| 8T5J | 2023 | 0 |
| 8T5N | 2023 | 0 |
| 8T5T | 2023 | 0 |
| 8T7W | 2023 | 0 |
| 8T7Z | 2023 | 0 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 6x79 | - | https://www.biorxiv.org/content/10.1101/2021.02.17.431625v1.abstract | A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features | 2021 | S Fatihi, S Rathore, A Pathak, D Gahlot, M Mukerji- bioRxiv, 2021 - biorxiv.org | Cryo-EM structures of the D614G spike structure have revealed that the mutant D614 is stable with RBD in an up mational states of the spike were analysed (see Methods for PDB ids) spike conformers showed large structural changes, with an average deviation of 2.77 0.42 ... 18 cryo-EM structures for closed spike conformation (PDB ID: 6ZGE, 6VXX, 6X2C, 6X6P, 6X29, 6X79, 6XF5, 6XLU, 6XM5, 6ZB4, 6ZB5, 6ZGI, 6ZP0, 7CAB, 7DDD, 7DF3, 7JJI and 7JWY) were taken from RCSB P |
| 2 | 6x79 | - | https://www.sciencedirect.com/science/article/pii/S0141813021015956 | Chitosan derivatives: A suggestive evaluation for novel inhibitor discovery against wild type and variants of SARS-CoV-2 virus | 2021 | C Modak, A Jha, N Sharma, A Kumar- International Journal of Biological, 2021 - Elsevier | of efficacious treatment strategies to robustly tackle this pandemic by targeting various pathways and mechanisms of infection by either creating new drug molecules or repurpose already existing drug molecules for impacting virus infection cycle or structural proteins [2] ... For heparan sulfate proteoglycan/heparin-binding site as target site, the homotrimerectodomain in prefusion state of S-glycoprotein PDB ID: 6X79 with a low resolution of 2.90 Å was considered |
| 3 | 6x79 | - | https://pubs.acs.org/doi/abs/10.1021/acsomega.0c03512 | Characterization of the SARS-CoV-2 S protein: biophysical, biochemical, structural, and antigenic analysis | 2020 | NG Herrera, NC Morano, A Celikgil, GI Georgiev- ACS, 2020 - ACS Publications | need to produce large quantities of high-quality SARS-CoV-2 Spike (S) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells... In nine structures that align well in this region (conformation 1: 6VXX, 6X29, 6X2C, 6X79, 6ZOX, 6ZOY, 6ZP0, 6ZP1, 6ZWV), the amino acid segment 621–640 was not modeled, presumably due to disorder |
| 4 | 6x79 | 7jv2 | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0252571 | Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors | 2021 | Baysal, N Abdul Ghafoor, RS Silme, AN Ignatov- PloS one, 2021 - journals.plos.org | The 3' end of the genome encodes 4 major structural proteins, including the spike protein (S), the nucleocapsid protein structure of refusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation ( PDB : 6X79 ), and X-ray diffraction structure of SARS |
| 5 | 6xdh | - | https://www.cell.com/structure/pdf/S0969-2126(22)00495-6.pdf | Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser | 2023 | RJ Jernigan, D Logeswaran, D Doppler, N Nagaratnam- Structure, 2023 - cell.com | using the crystal structure of NendoU PDB entry 6XDH as the search model (Dranow et al., unpublished results) with all solvent and ligand atoms removed. The structure was refined |
| 6 | 6xdh | - | https://academic.oup.com/bib/article-abstract/22/2/769/6067883 | SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets | 2021 | AF Alsulami, SE Thomas, AR Jamasb- Briefings in, 2021 - academic.oup.com | release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery, which also requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures , our group ... (v) Nsp15 (Uridylate specific endoribonuclease)—PDB Id: 6XDH. |
| 7 | 6xdh | - | https://www.biorxiv.org/content/10.1101/2021.06.02.446845v1.abstract | 3D-Scaffold: Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds. | 2021 | RP Joshi, N Gebauer, N Kumar, M Bontha- bioRxiv, 2021 - biorxiv.org | generates 3D coordinates of the molecules with a given core structure ; (II) It works equally 3 reasonable molecules even with small training datasets due to the robust architecture of the (Mpro) and a SARS-CoV-2 non- structural protein endoribonuclease (NSP15). ... As a test case example, we generated non-covalent inhibitors for the SAR-CoV-2 non-structural protein endoribonuclease (NSP15) target (PDB ID: 6XDH) by optimizing Exebryl-1 based compounds |
| 8 | 6xdh | - | https://academic.oup.com/bib/article-abstract/22/2/1476/6146769 | A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico | 2021 | A Rakib, Z Nain, SA Sami, S Mahmud- Briefings in, 2021 - academic.oup.com | Abstract. Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declar. ... For docking analysis, the following receptors were selected: PDB ID 6M3M for N protein, PDB ID 2GHV for the RBD of the S protein, PDB ID 6W9C for PLpro, PDB ID 6 M71 for RdRp, PDB ID 6ZSL for SARS-CoV-2 helicase (nsp13), 6WC1 for nsp9 RNA-replicase, and 6XDH for nsp15 |
| 9 | 7jv2 | 7k43, 7jva, 7km8 | https://www.science.org/doi/abs/10.1126/science.abh1139 | Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants | 2021 | M Yuan, D Huang, CCD Lee, NC Wu, AM Jackson- Science, 2021 - science.org | We therefore investigated the structural and functional 4 ( PDB 6XEY) (27) are shown in pink and light pink, respectively; S2M11 ( PDB 7K43) (30) in orange and yellow; C121 ( PDB 7K8X |
| 10 | 7jv2 | 7jva | https://www.cell.com/cell-reports/pdf/S2211-1247(21)01652-1.pdf | Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding | 2021 | D Mannar, JW Saville, X Zhu, SS Srivastava- Cell reports, 2021 - cell.com | See Table S2 for PDB entries included in this analysis. (D) Structural overlap of all antibodies selected on the SARSCoV-2 RBD. Mutational positions within the RBD are highlighted. (E) |