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 | 6q06 | - | https://www.biorxiv.org/content/10.1101/2021.04.14.439284v1.abstract | Cryptic SARS-CoV2-spike-with-sugar interactions revealed by'universal'saturation transfer analysis | 2021 | CJ Buchanan, B Gaunt, PJ Harrison, A Le Bas, A Khan- bioRxiv, 2021 - biorxiv.org | computational modelling environments provide exact structural models. In this way, uSTA analysis provides an automated pipeline from raw NMR free induction decay (FID) signals all the way to proteinligand structures in a freely available form for the non-expert |
| 2 | 3tmg | 4z9n, 4f3p | https://www.biorxiv.org/content/10.1101/2021.01.27.428399v1.abstract | Gating the channel pore of ionotropic glutamate receptors with bacterial substrate binding proteins | 2021 | M Bernhard, B Laube- bioRxiv, 2021 - biorxiv.org | The bacterial GluR0 receptor was chosen due to its less complex architecture compared to eukaryotic iGluRs, characterized by the lack of an NTD, a Therefore, we used the structure of the glutamate-bound closed GluR0-LBD conformation (Mayer et al., 2001) ( PDB ID |
| 3 | 6mg6 | - | https://www.tandfonline.com/doi/abs/10.1080/07388551.2020.1827367 | Nitrilase: a promising biocatalyst in industrial applications for green chemistry | 2021 | JD Shen, X Cai, ZQ Liu, YG Zheng- Critical Reviews in, 2021 - Taylor & Francis | 6I00), Saccharomyces cerevisiae ( PDB : 4H5U and 1F89), Pyrococcus abyssi ( PDB : 3KLC), Helicobacter pylori ( PDB : 6MG6 ) and Synechocystis ( PDB : 3WUY) has been obtained However, with most of the nitrilases, the crystal structure had been resolved, came from eukaryotes |
| 4 | 7lxy | 7ly2, 7lxz, 7ly3 | https://www.nature.com/articles/s41423-021-00752-2 | Neutralizing antibodies for the prevention and treatment of COVID-19 | 2021 | L Du, Y Yang, X Zhang- Cellular & Molecular Immunology, 2021 - nature.com | Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) initiates the infection process by binding to the viral cellular receptor angiotensin-converting enzyme 2 through the receptor-binding domain (RBD) in the S1 subunit of the viral spike (S) protein. ... a–e Cryo-EM structures of the SARS-CoV-2 S trimer bound to NTD-targeting nAbs a S2L28 (PDB 7LXZ), b S2M28 (PDB 7LY2), c S2X333 (PDB 7LXY), d 4-8 (PDB 7LQV), and e 4A8 (PDB 7C2L). |
| 5 | 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 |
| 6 | 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 |
| 7 | 4qji | - | https://www.nature.com/articles/s41467-020-20224-x | Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site | 2021 | V Mendes, SR Green, JC Evans, J Hess- Nature, 2021 - nature.com | Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis |
| 8 | 4kzk | - | https://link.springer.com/article/10.1007/s10930-021-09970-z | Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus | 2021 | JE Bae, IJ Kim, Y Xu, KH Nam- The protein journal, 2021 - Springer | of RmSBP, we performed comparative analysis and substrate docking studies using a previously reported crystal structure of SBP ( PDB code 5Z6V) as the initial model structure Among them, 9 models ( PDB codes: 3LFT, 2QH8, 5ER3, 4RS3, 4KZK , 5BRA, 3KSM, 2DRI |
| 9 | 4dz4 | - | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0248991 | Structure of the E. coli agmatinase, SPEB | 2021 | I Chitrakar, SF Ahmed, AT Torelli, JB French- Plos one, 2021 - journals.plos.org | The first stage used the default parameters with the structure of Burkholderia thailandensis hypothetical agmatinase ( 4DZ4 ) [34] as To place the ligand in the SPEB active site, the structure of the D. radiodurans agmatinase with bound hexane-1,6-diamine ( PDB code 1WOG |
| 10 | 6nb7 | 6nb6 | https://arxiv.org/abs/2101.01884 | Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein Through Molecular Dynamics Simulation | 2021 | Y Li, T Wang, J Zhang, B Shao, H Gong- arXiv preprint arXiv, 2021 - arxiv.org | taking the S proteins of SARS-CoV with 2 upward RBDs ( PDB ID: 6NB6) (21) and 3 upward RBDs ( PDB ID: 6NB7 ) (21) as We also conducted a time- structure based Independent Components Analysis (tICA) (34, 35) to identify slow motions with high time autocorrelation on |