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 |
|---|---|---|
| 6O3F | 2019 | 0 |
| 6O4N | 2019 | 0 |
| 6OE6 | 2019 | 0 |
| 6OHZ | 2019 | 0 |
| 6OKH | 2019 | 0 |
| 6ONN | 2019 | 0 |
| 6OR9 | 2019 | 0 |
| 6OTJ | 2019 | 0 |
| 6PI4 | 2019 | 0 |
| 6Q10 | 2019 | 0 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3qh4 | - | https://www.biorxiv.org/content/10.1101/2021.02.23.432567v1.abstract | Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber | 2021 | N Noby, R Johnson, J Tyzack, A Embaby, H Saeed- bioRxiv, 2021 - biorxiv.org | to fully open the HerE plug. LipW ( PDB 3QH4 ) (26) has two shorter residues in place PestE ( PDB 2YH2) (28) does not have the plug (Figure 2b). N211 is replaced by a of helical character than the WT suggesting a higher degree of structure for the mutant at this temperature |
| 2 | 6x79 | - | https://www.biorxiv.org/content/10.1101/2021.02.25.432861v3.abstract | Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS CoV-2 | 2021 | RC Penner- BioRxiv, 2021 - biorxiv.org | E of rotations of BHBs in HQ60; Table 1, Protein Data Bank structure files upon The methods of this paper are im- plented online from an uploaded PDB file at et al., Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture , Nature Communications, 5 |
| 3 | 6nb8 | - | https://www.biorxiv.org/content/10.1101/2021.04.12.439478.abstract | Epitope profiling of coronavirus-binding antibodies using computational structural modelling | 2021 | SA Robinson, MIJ Raybould, C Schneider, WK Wong- bioRxiv, 2021 - biorxiv.org | Analysis of SARS-CoV-2antibody structural complexes A total of 48 antibodies and 12 nanobodies had at least one published solved X-ray crystal structure in complex to the spike receptor binding domain (RBD, see Table S1 and Table S2 for names and PDB codes), while |
| 4 | 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 |
| 5 | 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 |
| 6 | 6xdh | - | https://www.biorxiv.org/content/10.1101/2021.06.02.446845v1.abstract | 3D-Scaffold: Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds. | 2021 | RP Joshi, N Gebauer, N Kumar, M Bontha- bioRxiv, 2021 - biorxiv.org | generates 3D coordinates of the molecules with a given core structure ; (II) It works equally 3 reasonable molecules even with small training datasets due to the robust architecture of the (Mpro) and a SARS-CoV-2 non- structural protein endoribonuclease (NSP15). ... As a test case example, we generated non-covalent inhibitors for the SAR-CoV-2 non-structural protein endoribonuclease (NSP15) target (PDB ID: 6XDH) by optimizing Exebryl-1 based compounds |
| 7 | 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 |
| 8 | 6tys | - | https://www.biorxiv.org/content/10.1101/2021.07.09.451785.abstract | Study of Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (Clustal-X) of Monoclonal mice/human antibodies | 2021 | IV Ferrari, P Patrizio- bioRxiv, 2021 - biorxiv.org | zone between 150-210 residues amino acids; with the exception of ID PDB 3I9G-3W9D 6TYS : (A potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah virus and Antibodies all have the same basic structure consisting of two heavy and two light |
| 9 | 5vbf | - | https://www.biorxiv.org/content/10.1101/2021.07.15.452591.abstract | The tetrameric assembly of 2-aminomuconic acid dehydrogenase is a functional requirement of cofactor NAD+ binding | 2021 | Q Shi, Y Chen, X Li, H Dong, C Chen, Z Zhong, C Yang- bioRxiv, 2021 - biorxiv.org | 144 The overall structure of AmnC protomers shares the general architecture of the ALDH 145 family (SSADH) ( PDB code:2W8P)(23-26). Pairwise superposition of the six protomers yielded 164 In this study, we elucidated the structure of AmnC and how it 260 |
| 10 | 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. |