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 |
|---|---|---|
| 3V8H | 2012 | 3 |
| 3LQW | 2010 | 3 |
| 3UWR | 2012 | 3 |
| 8DYA | 2022 | 3 |
| 4XI8 | 2016 | 3 |
| 4KZK | 2013 | 3 |
| 3GVF | 2009 | 3 |
| 5VP5 | 2017 | 3 |
| 8SLG | 2023 | 3 |
| 3FS2 | 2009 | 3 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3jvi | - | https://link.springer.com/protocol/10.1007/978-1-0716-0163-1_1 | In Silico Laboratory: Tools for Similarity-Based Drug Discovery | 2020 | S Lenik, J Konc- Targeting Enzymes for Pharmaceutical Development, 2020 - Springer | The output file 1phrA_3jviA.0.rota. pdb contains 3jvi's coordinates superimposed onto 1phr according to Information window contains the name, PDB , and UniProt number of the clicked amino acid Sequence variants that could not be mapped to the protein structure are listed |
| 2 | 3gmt | - | http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.919497 | Sampling large conformational transitions: adenylate kinase as a testing ground | 2014 | SL Seyler, O Beckstein - Molecular Simulation, 2014 - Taylor & Francis | Out of these structures only four (PDB IDs 4ake, 2rh5, 3umf, 3gmt) were crystallised in the apo form, i.e. in the absence of a substrate-like ligand, and these structures represent the open conformations of AdK. |
| 3 | 3urr | - | https://journals.asm.org/doi/abs/10.1128/jb.00023-23 | All dacs in a row: domain architectures of bacterial and archaeal diadenylate cyclases | 2023 | MY Galperin- Journal of Bacteriology, 2023 - Am Soc Microbiol | The search of the AlphaFold-predicted structure of DACNG using Dali (90) does not show any closely related structures in the PDB . This domain can also be found in a stand-alone ... PTS_EIIA_2 PF00359 139 3URR |
| 4 | 5eqz | - | https://hal.archives-ouvertes.fr/hal-01628162/ | Iterative Decomposition Guided Variable Neighborhood Search for Graphical Model Energy Minimization | 2017 | A Ouali, D Allouche, S De Givry- on Uncertainty in, 2017 - hal.archives-ouvertes.fr | Variable Neighborhood Search (VNS) (Mladenovic and Hansen, 1997) is a metaheuristic that uses a finite set of pre-selected neighborhood structures Nk,k = 1, 2, ..., kmax to escape from local minima by system- atically changing the neighborhood structure if the cur- rent one |
| 5 | 3uam | - | http://scripts.iucr.org/cgi-bin/paper?be5273 | Lytic polysaccharide monooxygenases: a crystallographer's view on a new class of biomass-degrading enzymes | 2016 | KEH Frandsen, L Lo Leggio - IUCrJ, 2016 - scripts.iucr.org | ... addi- tional evidence of the synergy between GH61 and cellulose- degrading glycoside hydrolaseswas presented, together with structure-based mutagenesis ... In the case of LPMOs structuralknowledge really can claim to have driven functional understanding. ... PDB code ASU ... |
| 6 | 4dz4 | - | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0248991 | Structure of the E. coli agmatinase, SPEB | 2021 | I Chitrakar, SF Ahmed, AT Torelli, JB French- Plos one, 2021 - journals.plos.org | The first stage used the default parameters with the structure of Burkholderia thailandensis hypothetical agmatinase ( 4DZ4 ) [34] as To place the ligand in the SPEB active site, the structure of the D. radiodurans agmatinase with bound hexane-1,6-diamine ( PDB code 1WOG |
| 7 | 3dms | - | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S17-S2 | Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases | 2012 | R Vinekar, C Verma, I Ghosh - BMC , 2012 - bmcbioinformatics.biomedcentral. | ... The current study therefore concentrates mainly on dimeric NADP-dependent IDHs from subfamilies I and II and additionally subfamily IV (Table 1), with an emphasis on regulation in dimeric M.tb IDH. Burcholderi apseudomallei BpIDH Q63WJ4_BURPS 3DMS. ... |
| 8 | 5k0s | - | https://www.jbc.org/article/S0021-9258(21)00446-4/abstract | Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium | 2021 | GF Mercaldi, M de Oliveira Andrade- Journal of Biological, 2021 - ASBMB | In addition, XcMetRS was compared with MetRS1 enzymes in complex with dual-site inhibitors from Trypanosoma brucei (PDB code: 4EGA) (48, 67), Brucella melitensis (PDB code: 5K0S) (35, 68), and S. aureus (PDB code: 4QRD) |
| 9 | 5bnt | - | https://scripts.iucr.org/cgi-bin/paper?dp5109 | Structure of aspartate -semialdehyde dehydrogenase from Francisella tularensis | 2018 | NJ Mank, S Pote, KA Majorek, AK Arnette- Section F: Structural, 2018 - scripts.iucr.org | entry 3pzr; Pavlovsky et al., 2012), Pseudomonas aeruginosa ( PDB entry 5bnt ; Seattle Structural N-acetyl- -glutamyl-phosphate reductases (ArgCs), including proteins with known structure : ArgCs from entry 2i3a; Cherney et al., 2007), Salmonella typhi- murium ( PDB entry 2g17 |
| 10 | 3sbx | - | https://www.nature.com/articles/s41598-017-12471-8 | A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis | 2017 | R Bhagavat, HB Kim, CY Kim, TC Terwilliger- Scientific reports, 2017 - nature.com | a given ligand recognition, and (d) sensitive methods are required to compare structural motifs against binding sites 33 and combine them into a workflow to obtain structure -based function a large-scale analysis of 4,766 ATP and other NTP binding proteins from PDB and have |