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 | 6wps | - | https://www.biorxiv.org/content/10.1101/2021.01.25.427846v1.abstract | SARS-CoV-2 receptor binding mutations and antibody mediated immunity. | 2021 | M Mejdani, K Haddadi, C Pham, R Mahadevan- BioRxiv, 2021 - biorxiv.org | 39 ( PDB : 7JMP), CV07- 250 ( PDB : 6XKQ), P2B-2F6 ( PDB : 7BWJ), CV07-270 ( PDB : 6XKP), BD-368-2 ( PDB : 7CHE), and S309 ( PDB : 6WPS ) 53 Laskowski, RA PDBsum: summaries and analyses of PDB structures Fig.1: Structure of SARS-CoV-2 RBD bound to ACE2 receptor |
| 2 | 6wps | 7jw0, 7k45, 7jx3, 7jv6, 7jva, 7jvc | https://pubs.rsc.org/en/content/articlehtml/2021/sc/d1sc01203g | Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies | 2021 | J Chen, K Gao, R Wang, GW Wei- Chemical science, 2021 - pubs.rsc.org | Our predictions are built from the X-ray crystal structure of SARS-CoV-2 S protein and ACE2 ( PDB 6M0J), 57 and various antibodies (PDBs 6WPS , 66 6XC2, 58 6XC3, 58 6XC4, 58 6XC7, 58 6XE1, 64 6XEY, 83 6XKP, 72 6XKQ, 72. |
| 3 | 6wps | 6vxx | https://academic.oup.com/nar/article-abstract/49/D1/D282/5901966 | CoV3D: a database of high resolution coronavirus protein structures | 2021 | R Gowthaman, JD Guest, R Yin- Nucleic acids, 2021 - academic.oup.com | (A) Visualization of the superposed spike RBD complexes with antibody S309 ( PDB code 6WPS ) ( 20 ) and (B) A trimeric spike structure in RBD-closed conformation ( 5 ) ( PDB code 6VXX Park YJ, Tortorici MA, Wall A., McGuire AT and Veesler D. (2020) Structure , Function, and |
| 4 | 6wps | - | https://www.nature.com/articles/s41598-020-71748-7 | Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition | 2020 | OC Grant, D Montgomery, K Ito, RJ Woods- Scientific reports, 2020 - nature.com | The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor Here we examine the structure of the SARS-CoV-2 envelope spike (S) protein that mediates host cell infection, with a. ... However, a closer examination also indicates a contraction between the 3D glycoform model and the observed binding of the neutralizing antibody S309 (PDB ID 6WPS). |
| 5 | 6wps | - | https://www.ncbi.nlm.nih.gov/pmc/articles/pmc7457611/ | Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies | 2020 | CO Barnes, CA Jette, ME Abernathy, KMA Dam- bioRxiv, 2020 - ncbi.nlm.nih.gov | 1g) that were isolated from the same donor 5 . They share structural similarities with each other and with other VH353/short 1) and C144 Fab (from C144-S structure ) aligned on a RBD monomer. ACE2 ( PDB 6M0J; light green surface) is aligned on the same RBD for reference ... Composite model of C135-RBD (blue and gray, respectively) overlaid with the SARS-CoV-2 NAb S309 (sand, PDB 6WPS) and soluble ACE2 |
| 6 | 6wps | 6wpt | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7586990/ | Immunological strategies against spike protein: Neutralizing antibodies and vaccine development for COVID19 | 2020 | J Huang, H Huang, D Wang, C Wang- Clinical and, 2020 - ncbi.nlm.nih.gov | Structural data of RBD of SARSCoV2 S protein with CR3022 Fab was retrieved from Protein Databank. (C) Structure of SARSCoV2 S protein with neutralizing antibody S309 Fab fragment ( PDB : 6WPS ) is shown in close state |
| 7 | 6wps | - | https://academic.oup.com/glycob/advance-article-abstract/doi/10.1093/glycob/cwab... | Modernized uniform representation of carbohydrate molecules in the Protein Data Bank | 2021 | C Shao, Z Feng, JD Westbrook, E Peisach- , 2021 - academic.oup.com | glycan structures (eg, SARS-CoV-2 protein-carbohydrate complex PDB ID 6WPS ) and the partnership is committed to maintaining consistency and accuracy across the PDB archive by regularly reviewing data processing procedures and carrying out structure remediation efforts |
| 8 | 6wpt | - | https://advances.sciencemag.org/content/7/16/eabf3671?utm_campaign=TrendMD_1&utm... | The SARS-CoV-2 spike variant D614G favors an open conformational state | 2021 | RA Mansbach, S Chakraborty, K Nguyen- Science, 2021 - advances.sciencemag.org | 1 Structural representation of the Spike protein. (A) The Spike complex is shown in the all-down conformation. Its S1 and S2 subunits are depicted in red and blue We display the domains highlighted in the Spike structure , shown from two different perspectives ... S309 Fab binding to up-RBD was modeled by rigid-body alignment to closed-RBD and Fab interactions from PDB structure 6WPT (21), using the backbone of residues 331 to 527 for least squares fitting. |
| 9 | 6wpt | - | https://hal.archives-ouvertes.fr/hal-03257466/document | Hyaluronic Acid-2-Deoxy-D-Glucose Conjugate Act as a Promising Targeted Drug Delivery Option for the Treatment of COVID-19 | 2021 | R Thirumalaisamy, V Aroulmoji- International, 2021 - hal.archives-ouvertes.fr | of 2DG and HA-2DG was submitted to Online SMILES convertor and Structure file generator proteases Mpro (6LU7), papain like protease PLpro (6W9C), spike protein ( 6WPT ), RNA dependent RNA polymerase (6M71) was retrieved from RCSB PDB database (https |
| 10 | 6wpt | - | https://www.sciencedirect.com/science/article/pii/S0165614720301668 | Fruitful neutralizing antibody pipeline brings hope to defeat SARS-Cov-2 | 2020 | A Renn, Y Fu, X Hu, MD Hall, A Simeonov- Trends in pharmacological, 2020 - Elsevier | and a receptor-binding subdomain also referred to as receptor binding motif (RBM, residues 438505) which loops out of the core domain structure to directly The structures used for superimposition of S309 and CR3022 are with RBD of SARS-CoV-2 ( PDB 6WPT [41] and |