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 |
|---|---|---|
| 5V0R | 2017 | 0 |
| 5V0U | 2017 | 0 |
| 5V77 | 2017 | 0 |
| 5VA8 | 2017 | 0 |
| 5VC2 | 2017 | 0 |
| 5VIX | 2017 | 0 |
| 8SKF | 2023 | 0 |
| 8SLD | 2023 | 0 |
| 8SLF | 2023 | 0 |
| 5VN6 | 2017 | 0 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 2kok | - | https://royalsocietypublishing.org/doi/abs/10.1098/rsfs.2019.0003 | A deep learning approach to the structural analysis of proteins | 2019 | M Giulini, R Potestio- Interface focus, 2019 - royalsocietypublishing.org | Second, we show that the application of a simple, standard and computationally not expensive DL architecture to the selected features gives satisfactory results, suggesting that The raw data employed in the present work, including PDB files, protein structure datasets, CNN ... Eigenvalues associated with 2KOK, 2YQD, and 1MEK were predicted with reasonable accuracy, the overall average MAPE being 30.7, 35.5 and 48.3, respectively. |
| 2 | 2lbb | 2l4b | https://arxiv.org/abs/1901.00991 | Physical Folding Codes for Proteins | 2019 | X Ma, C Hou, L Shi, L Li, J Li, L Ye, L Yang- arXiv preprint arXiv, 2019 - arxiv.org | 15 Soares, CM, Teixeira, VH & Baptista, AM Protein Structure and Dynamics in Nonaqueous Solvents: Insights from Nature Structural Biology 10, 980, doi:10.1038/nsb1203-980 (2003 JL The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data |
| 3 | 4k9d | - | https://link.springer.com/article/10.1007/s00436-019-06225-w | Identification and characterization of glyceraldehyde 3-phosphate dehydrogenase from Fasciola gigantica | 2019 | PB Chetri, R Shukla, T Tripathi- Parasitology research, 2019 - Springer | homologs, and the structure of the GAPDH of Brugia Malayi ( PDB ID: 4K9D ) was selected After validation, the modeled structure was used for binding site prediction. The binding site was predicted using the PDB structure co-crystallized with substrate and cofactor (Frayne et al |
| 4 | 5u25 | - | https://www.mdpi.com/2077-0383/8/12/2117 | FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function | 2019 | L Trisolini, N Gambacorta, R Gorgoglione- Journal of Clinical, 2019 - mdpi.com | Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure , although the investigated Similarly, AIF-crystallized structure hosts a FAD and two NADH molecules (4bur. pdb , [26]) and |
| 5 | 6q05 | - | https://www.sciencedirect.com/science/article/pii/S0022283620302874 | Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop | 2020 | JA Jaimes, NM Andr, JS Chappie, JK Millet- Journal of molecular, 2020 - Elsevier | Volume 432, Issue 10, 1 May 2020, Pages 3309-3325. Journal home page for Journal of Molecular Biology. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop |
| 6 | 5vog | - | https://scripts.iucr.org/cgi-bin/paper?ba5306 | ALIXE: a phase-combination tool for fragment-based molecular replacement | 2020 | C Milln, E Jimnez, A Schuster- Section D: Structural, 2020 - scripts.iucr.org | 2.4.1. Hypothetical protein ( PDB entry 5vog ). The crystal structure of a hypothetical protein from Neisseria gonorrhoeae with bound ppGpp was downloaded from the PDB ( PDB entry 5vog ; Seattle Structural Genomics Center for Infectious Disease, unpublished work) |
| 7 | 6vyb | - | https://pdfs.semanticscholar.org/7a8c/b4cb523ba6ce60d7e87c02e8558c13363b41.pdf | Comparative docking studies on curcumin with COVID-19 proteins | 2020 | R Suravajhala, A Parashar, B Malik, VA Nagaraj - 2020 - pdfs.semanticscholar.org | were subjected to a 3D structure generation on CORINA [12] using their SMILE Preparation of proteins and grid parameters: The protein data bank ( PDB ) structures of different proteins were retrieved from RCSB membrane protein (6M17), polymerase (6M71), spike ( 6VYB ) |
| 8 | 5k85 | - | https://onlinelibrary.wiley.com/doi/abs/10.1002/bio.3952 | Selective inhibition of Zophobas morio (Coleoptera: Tenebrionidae) luciferaselike enzyme luminescence by diclofenac and potential suitability for lightoff | 2020 | MC Carvalho, A Tomazini, RA Prado- Luminescence, 2020 - Wiley Online Library | tertiaricarbonis PDB file ID: 6HE0, Cryptococcus neoformans PDB file ID: 5K85 , Salmonella typhimurium PDB file ID: 5JRH) indicated that, among the five binding sites, that of CoA was structure and function prediction. Nat Protoc 2010; 5: 25-738. 49 |
| 9 | 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 |
| 10 | 2lwk | - | https://www.frontiersin.org/articles/10.3389/fchem.2020.00107/full?utm_source=S-... | Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting | 2020 | M Bissaro, M Sturlese, S Moro- Frontiers in Chemistry, 2020 - frontiersin.org | (B) Superimposition between the experimental NMR complex ( PDB ID 2LWK , green-colored DPQ (D) RMSD of RNA phosphate atoms belonging to the backbone, computed against the PDB reference. (E) Flexibility characterizing the RNA structure during DPQ binding event |