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 |
|---|---|---|
| 6CXM | 2018 | 0 |
| 6CY5 | 2018 | 0 |
| 6EEP | 2018 | 0 |
| 6EFW | 2018 | 0 |
| 6EFX | 2018 | 0 |
| 6MDY | 2018 | 0 |
| 6MFU | 2018 | 0 |
| 6MJK | 2018 | 0 |
| 5SCT | 2022 | 0 |
| 3UK2 | 2011 | 0 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 6c9e | - | https://www.biorxiv.org/content/10.1101/2020.05.24.113720v1.abstract | Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism | 2020 | RJ Nichols, B LaFrance, NR Phillips, LM Oltrogge- bioRxiv, 2020 - biorxiv.org | additional density for the holo-SrpI with a 243 homologous cysteine desulfurase dimer docked in ( pdb : 6c9e ) the first Family 2 encapsulin structure and is 267 the highest resolution structure for an Given the structural 271 similarity of the entire shell, it is unsurprising that the SrpI |
| 2 | 3tcq | - | https://www.biorxiv.org/content/10.1101/2020.05.27.108969v1.abstract | Common substructures and sequence characteristics of sandwich-like proteins from 42 different folds | 2020 | A Kister- BioRxiv, 2020 - biorxiv.org | structural classification in PDBSum database30 does not support sandwich-like architecture was examined. For secondary structure analysis, the information about localization of strands in sequences was taken from PDB .31 For supersecondary structure (SSS) of the domains |
| 3 | 3tjr | - | https://www.biorxiv.org/content/10.1101/2020.07.15.204123v2.abstract | On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment | 2020 | LM Longo, J Jablonska, P Vyas, R Kolodny, N Ben-Tal- bioRxiv, 2020 - biorxiv.org | between Rossmanns and P-loops, ideally with respect to not only structure but also sequence 2003.1.1.417; PDB : 1k2w) and short chain dehydrogenase (F-Group 2003.1.1.332; PDB : 3tjr ) showing the highest overlap (Figure 4) |
| 4 | 3eiy | - | https://www.biorxiv.org/content/10.1101/2020.07.15.204701v1.abstract | Graphein-a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures | 2020 | AR Jamasb, P Li, T Blundell- bioRxiv, 2020 - biorxiv.org | Figure 1. Example outputs from Graphein. A Example protein surface ( 3eiy ). B Example node feature matrix for the residue-level graphs outlined The interaction status data and structure originate from structures of the complexes in the RCSB PDB |
| 5 | 6bfu | 6q04, 6nb3, 6q05, 6q07, 6nb4, 6nb7, 6q06 | https://www.biorxiv.org/content/10.1101/2020.07.16.207308v3.abstract | Systematic modeling of SARS-CoV-2 protein structures | 2020 | SI O'Donoghue, A Schafferhans, N Sikta, C Stolte- bioRxiv, 2020 - biorxiv.org | CoV, 82% identity, E = 10-24) with a fold not seen in any other PDB structure (CATH 3.40 from SARS-CoV-2, 98% identity, E = 10-44), all with beta barrel architecture (CATH 2.40 6acg from SARS-CoV, 77% identity, E = 10-321), of which one structure also showed |
| 6 | 3sdo | - | https://www.biorxiv.org/content/10.1101/2020.08.24.261826v1.abstract | On the diversity of F420-dependent oxidoreductases: a sequence-and structure-based classification | 2020 | ML Mascotti, MJ Ayub, M Fraaije- bioRxiv, 2020 - biorxiv.org | monooxygenase (NTA_MO, PDB : 3sdo ), as well as the well-known bacterial FMN- dependent luciferases (eg.: LuxB, PDB : 1luc) [28]. The topology suggests that cofactor vary considerably in structure and function, and comprise the F420H2-NADP+ oxidoreductases |
| 7 | 3vab | - | https://www.biorxiv.org/content/10.1101/2020.10.01.322594v1.full-text | The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate | 2020 | VA Bielinski, JK Brunson, A Ghosh, MA Moosburner- bioRxiv, 2020 - biorxiv.org | in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA. ... Akin to protomer 2 of PtLYSA, this segment is not included in the structures of DAPDC from Aquifex aeolicus (PDB 2P3E) and Brucella melitensis (PDB 3VAB). |
| 8 | 4wny | - | https://www.biorxiv.org/content/10.1101/2020.10.03.324806v1.abstract | A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis | 2020 | A O'Connor, R Berisio, M Lucey, K Schaffer, S McClean- bioRxiv, 2020 - biorxiv.org | abilities. 253 To identify structural determinants responsible for the different behaviours of USP76 and 254 USP92, in particular their different abilities to bind to epithelial cells, we used homology 255 modelling and analysed resulting structures the best template was the BupsA stress protein from Burkholderia pseudomallei (PDB code 563 4wny, seqid 69.2%). |
| 9 | 3t7c | 3s55 | https://www.biorxiv.org/content/10.1101/2020.10.15.341941v1.abstract | Structural studies on M. tuberculosis decaprenyl phosphoryl--D-ribose epimerase-2 enzyme involved in cell wall biogenesis | 2020 | SP Gangwar, A Bandyopadhyay, AK Saxena- bioRxiv, 2020 - biorxiv.org | The MtbDprE2 structure was aligned with structures of PDB database using TM- structural alignment program of I-TASSER server, which yielded ten closest structural homologs (as coverage=97.2% [54] (vi) PDB - 3t7c , identity=13.3%, coverage=97.2% [55] (vii) PDB -1ipe |
| 10 | 2kn9 | - | https://www.biorxiv.org/content/10.1101/2020.10.27.356691v1.abstract | A new twist of rubredoxin function in M. tuberculosis | 2020 | T Sushko, A Kavaleuski, I Grabovec, A Kavaleuskaya- bioRxiv, 2020 - biorxiv.org | 21]. Previously, a zinc-substituted RubB structure was solved by NMR ( PDB ID: 2KN9 ). Pairwise . In the NMR model, residues at C and N termini show backbone variability, while the rest of the structure remain almost unperturbed |