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 |
|---|---|---|
| 3HZU | 2009 | 4 |
| 7L4G | 2020 | 4 |
| 4F3P | 2012 | 4 |
| 4F4F | 2012 | 4 |
| 4O5O | 2014 | 4 |
| 4EYE | 2012 | 4 |
| 7JXD | 2020 | 4 |
| 3Q8N | 2011 | 4 |
| 7K6C | 2021 | 4 |
| 3I0P | 2009 | 4 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 4iuj | - | http://www.nature.com/nature/journal/v527/n7576/abs/nature15525.html | Crystal structure of the RNA-dependent RNA polymerase from influenza C virus | 2015 | N Hengrung, K El Omari, IS Martin, FT Vreede - Nature, 2015 - nature.com | ... he published fragments of FluPolA (PDB accessions 4IUJ, 4AWH, 4CB4, 3A1G and 2VY7) were fitted by eye using Coot, which was used for all model building. ... |
| 2 | 6nb6 | - | https://www.biorxiv.org/content/10.1101/2020.04.03.024885v1.abstract | Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing | 2020 | T Desautels, A Zemla, E Lau, M Franco, D Faissol- BioRxiv, 2020 - biorxiv.org | In the absence of a known SARS-CoV-2 spike protein structure , we characterized the SARS-CoV- 2 surface glycoprotein sequence YP_009724390.1 [13 The structures of the spike proteins from SARS-CoV-1 (Protein Data Bank ( PDB ) entries: 5x58 [15], 6nb6 [10], 2dd8 [11 |
| 3 | 4ohc | - | https://pubs.acs.org/doi/abs/10.1021/acscatal.9b05294 | Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by means of X-ray Crystallography and Computational Simulations | 2020 | M Roca, S Navas-Yuste, K Zinovjev- ACS, 2020 - ACS Publications | Then, the dimeric architecture of OPRTase plays an essential role in the catalysis since The coordinates and structure factors have been deposited in the Protein Data Bank ( PDB ) with accession codes 6TAI (EcOPRT), 6TAJ (EcOPRT/OA) and 6TAK (EcOPRT/OA/SO4 2-). 2.5 |
| 4 | 3dmo | - | http://onlinelibrary.wiley.com/doi/10.1002/pro.2863/full | Crystal structures of MBP fusion proteins | 2015 | DS Waugh - Protein Science, 2015 - Wiley Online Library | ... 65 Nineteen of the MBP fusion protein structures deposited in the PDB include surface ... Table 2. Surface Entropy Reduction Mutations in MBP and Their Participation in Crystal Contacts 3DMO D83A/K84A ... |
| 5 | 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. |
| 6 | 3gmt | - | http://onlinelibrary.wiley.com/doi/10.1002/prot.22995/full | Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches | 2011 | D Armenta-Medina, E P?rez-Rueda? - Proteins: Structure, Function, and Bioinformatics, 2011 - Wiley Online Library | ... PDB ID, Organism, Resolution ?, Chain, %ID. 4ake, Escherichia coli, 2.20, A, 100. 3be4, Cryptosporidium parvum, 1.60, A, 45. 3fb4, Marinibacillus marinus, 2.00, A, 49. 3gmt, Burkholderia pseudomallei, 2.10, B, 66. 2c9y, Homo sapiens, 2.10, A, 49. 1ak2, Bos taurus, 1.92, A, 48. ... |
| 7 | 3ijp | 4ywj, 4f3y | https://www.sciencedirect.com/science/article/pii/S0006291X18316516 | 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae structure and interactions with coenzymes and substrate analog | 2018 | S Pote, SE Pye, TE Sheahan- Biochemical and, 2018 - Elsevier | In case of NgDapB, the position of the coenzyme is modeled using structure of PaDapB ( PDB ID from Bartonella henselae, Burkholderia thailandensis, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Thermotoga maritima ( PDB IDs: 3IJP , 4F3Y, 1ARZ, 4YWJ, 3QY9, 1VM6). |
| 8 | 4jv3 | 4f32 | https://pubs.acs.org/doi/abs/10.1021/acsmedchemlett.0c00653 | Semisynthesis and Biological Evaluation of Platencin Thioether Derivatives: Dual FabF and FabH Inhibitors against MRSA | 2021 | Y Li, X Weng, Y Deng, J Pan, S Zhu- ACS medicinal, 2021 - ACS Publications | The discovery and clinical use of multitarget monotherapeutic antibiotics is regarded as a promising approach to reduce the development of antibiotic resistance. Platencin (PTN), a potent natural a... On the basis of the X-ray structures of PTN with ecFabF(C163Q), Burkholderia vietnamiensis FabF, and Brucella melitensis FabB (PDB IDs 3HO2, 4F32, and 4JV3, respectively) as well as that of platencin A1 with ecFabF-(C163Q) (PDB ID 3HO9), it is likely that these PTN derivatives may also interact with FabF or |
| 9 | 3obk | - | http://www.ingentaconnect.com/content/ben/ctmc/2013/00000013/00000001/art00006 | Impact of quaternary structure dynamics on allosteric drug discovery | 2013 | EK Jaffe - Current topics in medicinal chemistry, 2013 - ingentaconnect.com | ... Toxoplasma gondii PBGS (PDB id 3OBK, shown left) contains a 13 amino acid C-terminal exten- sion that forms a domain swapped beta sheet (orange/yellow), which locks the dimer into the pro-octamer conformation. Pseudomonas ... |
| 10 | 4o5o | - | https://academic.oup.com/peds/article-abstract/doi/10.1093/protein/gzab008/62691... | A fragment-based protein interface design algorithm for symmetric assemblies | 2021 | J Laniado, K Meador, TO Yeates- Protein Engineering, Design, 2021 - academic.oup.com | The expansive database of known protein structures provides valuable empirical frameworks for The growing focus on secondary structure associations motivates an attempt to bring by precomputing common proteinprotein fragment configurations from known structural data |