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 |
|---|---|---|
| 3JVH | 2009 | 8 |
| 3JVI | 2009 | 4 |
| 3K14 | 2009 | 7 |
| 3K2C | 2009 | 4 |
| 3K2H | 2009 | 11 |
| 3K2X | 2009 | 4 |
| 3K5P | 2009 | 3 |
| 3K9G | 2009 | 8 |
| 3K9W | 2009 | 7 |
| 3KC6 | 2010 | 9 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3ecd | - | http://onlinelibrary.wiley.com/doi/10.1111/febs.13211/abstract | How pyridoxal 5'‐phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state | 2015 | G Giardina, P Brunotti, A Fiascarelli, A Cicalini… - FEBS …, 2015 - Wiley Online Library | ... shows a completely open conformation of the dimer (PDB id: 3ecd), as in the case of apo-SHMT2 ...method using the apo-enzyme (PDB: 3ou5) as search model in MOLREP [54 ... F, Morea V,Angelaccio S, Saccoccia F, Contestabile R & Ilari A (2014) The crystal structure of archaeal ... |
| 2 | 3eg4 | - | http://www.sciencedirect.com/science/article/pii/S0022283609004914 | The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism | 2009 | L Schuldt, S Weyand, G Kefala, MS Weiss - Journal of molecular biology, 2009 - Elsevier | ... coli (PDB entry 3BXY), 7 Campylobacter jejuni (PDB entry 2RIJ, Joint Center for Structural Genomics, unpublished results), Enterococcus faecalis (PDB entry 3CJ8, K. Tan et al., unpublished results) and Brucella melitensis biovar abortus (PDB entry 3EG4, Seattle Structure ... |
| 3 | 3eg4 | 3mdx, 3qxi, 3lqw, 3laa, 3oc7 | http://www.theses.fr/2015GRENM005/abes | Nouvelles méthodes de calcul pour la prédiction des interactions protéine-protéine au niveau structural | 2015 | P Popov - 2015 - theses.fr | ... au niveau structural Thèse soutenue publiquement le « 28 Janvier 2015 », devant le jury composéde : ... blue, respectively). Right: native structure of Target 58 (grey) and medium-quality model pro- ...18 2.2 Query protocols for the PDB that were used to compose the bound bench- ... |
| 4 | 3eg4 | - | http://dx.plos.org/10.1371/journal.pone.0031133 | Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion | 2012 | R Schnell, W Oehlmann, T Sandalova, Y Braun? - PloS one, 2012 - dx.plos.org | ... In addition, the coordinates for DapD from Campylobacter jejuni (2RIJ), Enterococcus feacalis (3CJ8), Brucella melitensis (3EG4), and Yersinia ... model of the trimer of the putative tetrahydropyridine-2-carboxylate N-succinyltransferase from Campylobacter jejuni (PDB code ... |
| 5 | 3eiy | - | https://academic.oup.com/bib/article-abstract/22/6/bbab159/6278145 | Utilizing graph machine learning within drug discovery and development | 2021 | T Gaudelet, B Day, AR Jamasb, J Soman- Briefings in, 2021 - academic.oup.com | structural relationships between their amino acid residues [19, 20] and small molecule drugs as graphs relating their constituent atoms and chemical bonding structure [ data structures . Figure 7. Illustration of (A) a protein (PDB accession: 3EIY) and (B) its graph representation derived based on intramolecular distance with cut-off threshold set at 10Å. |
| 6 | 3eiy | - | http://www.sciencedirect.com/science/article/pii/S1570963914001095 | Asn112 in< i> Plasmodium falciparum</i> glutathione S-transferase is essential for induced reversible tetramerization by phosphate or pyrophosphate | 2014 | I Quesada-Soriano, C Barn, R Tllez-Sanz - et Biophysica Acta (BBA , 2014 - Elsevier | ... the alignment between one of the docking poses for the binding of pyrophosphate to the PfGST tetramer near the Asn112–Lys117 closed-square pattern and three of the pyrophosphatase structures (3Q4W from Thermococcus thioreducens, 3EIY from Burkholderia pseudomallei and 2AUU/1I6T from E. coli), is suspiciously good. ... |
| 7 | 3eiy | - | https://arxiv.org/abs/2012.05716 | Utilising Graph Machine Learning within Drug Discovery and Development | 2020 | T Gaudelet, B Day, AR Jamasb, J Soman- arXiv preprint arXiv, 2020 - arxiv.org | and evolve along a temporal dimension resulting in changes to composition, structure and attributes One such approach is to use a graph's structural information to regularise embeddings authors suggest the atten- tion mechanism is decoupled from the architecture and should |
| 8 | 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 |
| 9 | 3eiz | 3i4t | http://www.turkjbiochem.com/2014/435-442.Ek2.pdf | High pKa variability of cysteine residues in structural databases and the effect of H-bond contributions | 2014 | SM Marino, İ Soylu - Türk Biyokimya Dergisi [Turkish Journal of …, 2014 - turkjbiochem.com | ... High pKa variability of cysteine residues in structural ... RESULTS of ppka3 on PDB-crystal datasetprot=protein name res_num=residue number H-bond=hydrogen bond contribution to pKaprediction (pKa) Coul=electrostatics (from Coulombic interactions) contribution to pKa ... |
| 10 | 3eiz | - | http://www.sciencedirect.com/science/article/pii/S0968089614004337 | Influence of azide incorporation on binding affinity by small papain inhibitors | 2014 | AEM Wammes, TG Hendriks - Bioorganic & medicinal , 2014 - Elsevier | ... 20 (b) Docking of leupeptin in the active site of papain (PDB file 1POP). ... 21 Prior to docking we investigated different papain structures of the PDB to explore different ligandpapain complexes, as well as the flexibility of the protein in the area of the binding site. ... |