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 |
|---|---|---|
| 8T7Z | 2023 | 0 |
| 8T7W | 2023 | 0 |
| 8T5T | 2023 | 0 |
| 8T5N | 2023 | 0 |
| 8T5J | 2023 | 0 |
| 8T1A | 2023 | 0 |
| 8SWD | 2023 | 0 |
| 8SU6 | 2023 | 0 |
| 8SQT | 2023 | 0 |
| 8SQR | 2023 | 0 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 8slg | - | https://www.nature.com/articles/s41467-024-48837-6 | Structure prediction of protein-ligand complexes from sequence information with Umol | 2024 | P Bryant, A Kelkar, A Guljas, C Clementi- Nature, 2024 - nature.com | We parsed all protein sequences from the PDB files. 18884 out of 19119 protein structures (99%) could be parsed (<80% missing CAs and >50 residues). Only the first protein chain in |
| 2 | 8dya | - | https://www.nature.com/articles/s41467-024-49656-5 | A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines | 2024 | J Lee, C Stewart, A Schfer, EM Leaf, YJ Park- Nature, 2024 - nature.com | (Right) SARS-CoV-2 S ( PDB 6VXX) colored by sequence conservation across multiple the C-44 cryoEM structure previously determined with splayed open apex 17 ( PDB 8DYA ). c Size- |
| 3 | 8dp2 | - | https://www.nature.com/articles/s41467-024-45632-1 | Poly--glutamylation of biomolecules | 2024 | G Bashiri, EMM Bulloch, WR Bramley- Nature, 2024 - nature.com | To produce an FPGS ligand model, MurD, FolC, and FPGS crystal structure coordinates (2UAG, 4UAG, 8DP2, 1W78, and 2VOR) were downloaded from the Protein Data Bank ... structures were overlaid using COOT and appropriate ligands appended to the FPGS structure as indicated by structural and intermolecular contacts in PDB structures 8DP2 and 4UAG, |
| 4 | 7sof | - | https://www.cell.com/immunity/fulltext/S1074-7613(25)00178-5 | Computationally designed proteins mimic antibody immune evasion in viral evolution | 2025 | N Youssef, S Gurev, F Ghantous, KP Brock, JA Jaimes- Immunity, 2025 - cell.com | Figure 3... . The impact of K147 mutations can be seen for NTD antibody S2X303, with interactions to N65, D50, and Y31 on the antibody (PDB: 7SOF). |
| 5 | 7so9 | - | https://www.nature.com/articles/s41421-023-00535-1 | Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants | 2023 | X Chi, L Xia, G Zhang, X Chi, B Huang, Y Zhang- Cell Discovery, 2023 - nature.com | with multiple structures , we selected the subcomplex deposited earliest in the PDB database ID: 7SO9 ) were manually refined based on the focused-refined cryo-EM map. Each residue |
| 6 | 7so9 | - | https://dergipark.org.tr/en/pub/biotechstudies/issue/77337/1332403 | Omicron variants bind to human angiotensin-converting enzyme 2 (ACE2) much stronger due to higher number of charged-charged interactions | 2023 | S Kalyoncu- Biotech Studies - dergipark.org.tr | Three dimensional RBD domain structures of many variants used in this study were already in RCSB PBD database ( PDB IDs: 7EKF for Alpha, 7EKG for Beta, 7EKC for Delta, 7SO9 for |
| 7 | 7so9 | - | https://www.nature.com/articles/s42003-024-07350-8 | The identification of a SARs-CoV2 S2 protein derived peptide with super-antigen-like stimulatory properties on T-cells | 2025 | TH Tu, FE Bennani, N Masroori, C Liu- Communications, 2025 - nature.com | PDB IDs: 2XN9 62 and 4C56 63 were used, 2XN9 and 4C56 were attached with two crystal structures the complex HLA I-TCR, we used the PDB IDs 3PWP 64 . ... PDB IDs of the variants of SARS-CoV 2 used for homology modeling: Alpha_(B.1.1.7) (7R1A), Beta_(B.1.351) (7Q6E), Gamma_(P.1) (7V83), Delta_(B.1.617.2) (7SO9), Omicron_(B.1.529) (7WPA). |
| 8 | 7sh3 | - | https://www.nature.com/articles/s42004-023-01029-7 | Peptide binder design with inverse folding and protein structure prediction | 2023 | P Bryant, A Elofsson- Communications Chemistry, 2023 - nature.com | ProteinMPNN was trained on assemblies in the PDB these to unique PDB IDS, one finds 4086 PDB IDS in total. from all PDB IDs and extracted interacting pairs (one per PDB ID) based ... To see if the modification of the AF protocol described here can distinguish these binders, we analyse sequences tested against four different receptor proteins with solved receptor-binder structures ... IL7Ra: https://www.rcsb.org/structure/7OPB and VirB8:https://www.rcsb.org/structure/7SH3). |
| 9 | 7ral | - | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10769253/ | Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates | 2023 | RD Malewana, V Stalls, A May, X Lu, DR Martinez- bioRxiv, 2023 - ncbi.nlm.nih.gov | Our structural studies identified the DH1193 epitope as one of these conserved epitopes on in PDB : 8DPZ, 8DTK, 7RAL . Materials are available with a Materials transfer agreement. |
| 10 | 7ral | - | https://www.science.org/doi/abs/10.1126/scitranslmed.adn5651 | Nonstabilized SARS-CoV-2 spike mRNA vaccination induces broadly neutralizing antibodies in nonhuman primates | 2025 | RD Malewana, V Stalls, A May, X Lu- Science Translational, 2025 - science.org | Our structural studies identified the DH1193 epitope as one of these conserved epitopes on accession numbers 8DPZ, 8DTK, and 7RAL in the PDB . Biospecimens, proteins, DNA, and |