SSGCID
Seattle Structural Genomics Center for Infectious Disease

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

Manually reviewed citations

# PDB Additional SSGCID structures cited Link Title Year Citation Highlighted abstract
1 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
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://www.biorxiv.org/content/10.1101/2021.02.25.432861v3.abstract Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS CoV-2 2021 RC Penner- BioRxiv, 2021 - biorxiv.org E of rotations of BHBs in HQ60; Table 1, Protein Data Bank structure files upon The methods of this paper are im- plented online from an uploaded PDB file at et al., Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture , Nature Communications, 5
4 6x79 - https://www.biorxiv.org/content/10.1101/2021.05.06.441046v1.abstract Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity 2021 E Olmedillas, CJ Mann, W Peng, YT Wang, RD Avalos- bioRxiv, 2021 - biorxiv.org For VFLIP_D614G, a population of 213,852 particles yielded a 2.8 resolution structure (Figure S2). Importantly, the density maps confirm Further sub-classification revealed an overall architecture that is similar to other closed spikes in the Protein Data Bank ( PDB ). ... A previously published structure of the SARS-CoV-2 ectodomain with all RBDs in the down conformation (PDB ID 6X79) was used to fit the cryo-EM maps in UCSF ChimeraX
5 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
6 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
7 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.
8 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
9 7jv2 7jvc, 7jw0, 7ra8, 7ral https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010260 Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants 2022 A Mittal, A Khattri, V Verma- PLoS Pathogens, 2022 - journals.plos.org Recent structural and functional studies have mapped the -CoV-2 variants; (2) the structural basis for antibody-mediated fitness, and in conjunction with the structures of the spike-nAb ... the neutralization mechanism involves direct competition with the ACE2 receptor. These antibodies include C002 (PDB: 7K8S) [70], C104 (PDB: 7K8U) [70], S2H13 (PDB: 7JV2) [77], C119 (PDB: 7K8U) [70], C121 (PDB: 7K8X) [70], LY-CoV555 (PDB: 7KMG), DH1041 (7LAA), COVA2-15 (EMD-22061) [82], 2–43 (EMD-22275) [94],
10 7jv2 7jx3 https://pubs.acs.org/doi/abs/10.1021/acscentsci.1c00216 Molecular Aspects Concerning the Use of the SARS-CoV-2 Receptor Binding Domain as a Target for Preventive Vaccines 2021 Y Valdes-Balbin, D Santana-Mederos- ACS Central, 2021 - ACS Publications The development of recombinant COVID-19 vaccines has resulted from scientific progress made at an unprecedented speed during 2020. The recombinant spike glycoprotein monomer, its trimer, and its re... Structural analyses were performed from PDB: 6M0J for the complex ACE2–RBD, (9) PDB: 7BZ5 for B38, (85) PDB: 7BYR for BD23, (86) PDB: 6XEY for Fab2-4, (87) PDB: 7BWJ for P2B-2F6, (88) PDB: 7JV2 for S2H13