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 | 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 |
| 2 | 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], |
| 3 | 7jva | - | https://www.nature.com/articles/s41467-023-35949-8.pdf | Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2 | 2023 | KYA Huang, X Chen, A Mohapatra- Nature, 2023 - nature.com | PDB code 7M7B for 3D11 and 7JVA for S2A4. c IS-9A and similar antibodies extend their footprints upwards and contact residue 408 and the residues 502-504 region. |
| 4 | 7jw0 | - | https://www.nature.com/articles/s41586-022-04980-y | BA. 2.12. 1, BA. 4 and BA. 5 escape antibodies elicited by Omicron infection | 2022 | Y Cao, A Yisimayi, F Jian, W Song, T Xiao, L Wang- Nature, 2022 - nature.com | Here, coupled with structural comparisons of the spike proteins, we show that BA.2.12.1, BA.4 and BA.5 (BA.4 and BA.5 are hereafter referred collectively to as BA.4/BA.5) exhibit similar ... b, Epitope of representative antibodies in group E3 (S2H97, PDB: 7M7W) and F1 (S304, PDB: 7JW0). Residues highlighted in red indicate mutated sites in Omicron variants. |
| 5 | 7jw0 | - | https://pubs.acs.org/doi/abs/10.1021/acs.jctc.1c00372 | Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based | 2021 | G Verkhivker, S Agajanian, D Oztas- Journal of Chemical, 2021 - ACS Publications | The functional adaptability and conformational plasticity of SARS-CoV- 2 spike proteins allow for the efficient modulation of complex phenotypic responses to the host receptor and antibodies. In thi... |
| 6 | 7jwk | 6mu0 | https://www.sciencedirect.com/science/article/pii/S002228362100588X | Building structural models of a whole mycoplasma cell | 2022 | M Maritan, L Autin, J Karr, MW Covert, AJ Olson- Journal of molecular, 2022 - Elsevier | PDB structure for a specific ingredient. Proteins with high sequence similarity and structural ... Ten of these experimental structures were used in our spatial model for the following gene products: MG396 (RpiB, 6MU0), MG027 (NusB, 1Q8C), MG191 .... The other four genes are only partially captured by experimentally-determined structures: MG200 (DnaJ-like, 4DCZ), MG238 (tig, 1HXV), MG301 (GapA, 7JWK), and MG469 (DnaA, 2JMP). |
| 7 | 7jx3 | 7k3q, 7r7n | https://www.nature.com/articles/s41586-021-03807-6 | SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape | 2021 | TN Starr, N Czudnochowski, Z Liu, F Zatta, YJ Park- Nature, 2021 - nature.com | An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape13, have activity against diverse sarbecoviruses47, and be highly protective through viral neutralization... Structures used were those described in this paper, or previously published structures: ACE2-bound RBD (6M0J)60, CR3022-bound RBD (6W41)61, REGN10987- and REGN10933-bound RBD (6XDG)62, CB6- (LY-CoV016) bound RBD (7C01)63, and S304, S309 and S2H14-bound RBD (7JX3)15. |
| 8 | 7jxc | 7jxe, 7jxd | https://www.sciencedirect.com/science/article/pii/S0092867421000805 | Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity | 2021 | EC Thomson, LE Rosen, JG Shepherd, R Spreafico- Cell, 2021 - Elsevier | / pdb /surface_glycoprotein/SARS-CoV-2/6m0j/isolde/notes.txt. The 1r42 refined structure differs from the PDB -deposited structure (copied from the 6m17 PDB structure ). ... Key resources table S2H13, S2H14, S2A4, S2X35 IgG Piccoli et al., 2020 PDB: 7JV2, 7JXC, 7JXD, 7JXE |
| 9 | 7jzl | 7jzn | https://www.biorxiv.org/content/10.1101/2021.06.15.448568v1.abstract | Deep Mutational Scanning of Dynamic Interaction Networks in the SARS-CoV-2 Spike Protein Complexes: Allosteric Hotspots Control Functional Mimicry and | 2021 | G Verkhivker- bioRxiv, 2021 - biorxiv.org | pdb id 7KL9 (A), in the complex with the designed miniprotein binder LCB1, pdb id 7JZL (B) complex with the miniprotein LCB3, pdb id 7JZN (C). The structure is in ribbons with protomers A,B,C are colored in green, red and blue respectively |
| 10 | 7jzl | - | https://www.sciencedirect.com/science/article/pii/S0022283621003892 | A brief history of de novo protein design: minimal, rational, and computational | 2021 | DN Woolfson- Journal of Molecular Biology, 2021 - Elsevier | For comparison, the whole PDB is doubling in size approximately every 67 years. There are now over 100 structures of de novo peptides and proteins, which is a good resource ... Figure 2. A gallery of high-resolution de novo designed peptide and protein structures .. additional protein chains are shown in grey these are for protein fusions to the designs (6FES99) or with targeted protein-protein interactions (4OYD,5VID,6IWB,6XXV,7JZL,6YWC) |