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.
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 5ji5 | - | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080978.3/ | Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches | 2021 | G Selvaraj, S Kaliamurthi, GH Peslherbe- F1000Research, 2021 - ncbi.nlm.nih.gov | Structural modeling approach to study host-SARS-CoV-2 proteins interaction and drug and similarity and with the highest resolution template automatically from PDB and then Then, the corresponding structures constructed by superimposing the modeled protein structure on to |
| 2 | 6vxx | - | https://academic.oup.com/nar/article-abstract/49/D1/D437/5992282 | RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental | 2021 | SK Burley, C Bhikadiya, C Bi, S Bittrich- Nucleic acids, 2021 - academic.oup.com | Biology; Nucleic Acid Enzymes; RNA and RNA-protein complexes; Structural Biology; Synthetic Biology and Bioengineering; Methods Online; Surveys and Summaries; Database; Web Server. Advance articles; Submit: Author Guidelines; |
| 3 | 6q04 | - | https://link.springer.com/article/10.1007/s00705-021-04961-y | A comparative study of human betacoronavirus spike proteins: structure, function and therapeutics | 2021 | J Verma, N Subbarao- Archives of virology, 2021 - Springer | Coronaviruses are the paradigm of emerging 21st century zoonotic viruses, triggering numerous outbreaks and a severe global health crisis. The current COVI. |
| 4 | 6ok4 | 4lsm, 4k9d | https://www.sciencedirect.com/science/article/pii/S0300908421000249 | Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth | 2021 | S Boreiko, M Silva, J Iulek- Biochimie, 2021 - Elsevier | The GAPDH’s structures selected for sequence alignment were from: Brugia malayi, Bmal - PDB ID: 4K9D ... and Chlamydia trachomatis, Ctra - PDB ID: 6OK4 [66] |
| 5 | 5tw7 | - | https://www.mdpi.com/2079-7737/10/7/594 | Discovery of Novel GMPS Inhibitors of Candidatus Liberibacter Asiaticus by Structure Based Design and Enzyme Kinetic | 2021 | J Nan, S Zhang, P Zhan, L Jiang- Biology, 2021 - mdpi.com | SwissModel was employed to generate the three-dimensional structure of CLas GMPS using Neisseria gonorrhoeae GMPS ( PDB ID: 5TW7 ) as a The homology model of the CLas GMPS structure was a dimer (Figure 1). The quality of the three-dimensional structure of CLas |
| 6 | 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 |
| 7 | 5vcu | - | https://arxiv.org/abs/2102.03202 | Interpretable Neural Networks based classifiers for categorical inputs | 2021 | S Zamuner, PDL Rios- arXiv preprint arXiv:2102.03202, 2021 - arxiv.org | cartoon representation of RAS protein (green) bounded to GDP (light blue spheres) from pdb 5vcu belonging to the most relevant predicted triplets are clustered in the structure of the Note that, to better compare to plmDCA, the same architecture and hyperparameters have |
| 8 | 6u94 | - | https://www.biorxiv.org/content/10.1101/2021.08.17.456619.abstract | Genome sequencing of 196 Treponema pallidum strains from six continents reveals additional variability in vaccine candidate genes and dominance of Nichols clade | 2021 | NAP Lieberman, MJ Lin, H Xie, L Shretha, T Nguyen- bioRxiv, 2021 - biorxiv.org | guided by the top 1-7 templates for each target. We used the following templates in modelling each target: TP0136 used 4a2l and 5oj5; TP0326 used 4k3b and 5d0o; TP0548 used 6h3i; TP0966 used 1yc9, 3d5k, 4k7r, 4mt0, 4mt4, 5azs, and 6u94; TP0967 used 1yc9, 3d5k, 5azp, 5azs, and 6u94. |
| 9 | 7lxz | 7ly2 | https://www.cell.com/cell-reports/pdf/S2211-1247(21)01401-7.pdf | Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain | 2021 | G Cerutti, Y Guo, P Wang, MS Nair, M Wang, Y Huang- Cell reports, 2021 - cell.com | We produced a structural superposition of all NTD-directed antibodies deposited in the PDB , superposed on NTD Ca atoms, in the context of SARS-CoV-2 spike trimer (Figure 2A). ... Figure S1. Sequence alignment for 5-7 with their corresponding germline genes, Related to Figures 1 and 2. 7LXZ McCallum et al., 2021 |
| 10 | 5k0s | - | https://www.jbc.org/article/S0021-9258(21)00446-4/abstract | Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium | 2021 | GF Mercaldi, M de Oliveira Andrade- Journal of Biological, 2021 - ASBMB | In addition, XcMetRS was compared with MetRS1 enzymes in complex with dual-site inhibitors from Trypanosoma brucei (PDB code: 4EGA) (48, 67), Brucella melitensis (PDB code: 5K0S) (35, 68), and S. aureus (PDB code: 4QRD) |