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.
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3swt | - | https://www.biorxiv.org/content/10.1101/2021.01.05.425418v1.abstract | Virus-associated organosulfur metabolism in human and environmental systems | 2021 | K Kieft, AM Breister, P Huss, AM Linz, E Zanetakos- bioRxiv, 2021 - biorxiv.org | oxygen binding (eg WH and H) (Knauer 198 et al., 2012). Conserved amino acid residues that are not functional are likely preserved for 199 structural features. The retention of AMGs on viral genomes despite strong selective ... Annotations of functional amino acid residues were labeled according to the Protein Data Bank (PDB, accessed January 2019) (Berman et al., 2000) with the following identification numbers: 4BZQ and 4BZP (CysC), 2GOY (CysH), 3ZEI (CysK), 3SWT (TauD), and 1RG9 (MetK). |
| 2 | 4ol9 | 4qji | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7770189/ | Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents | 2020 | HS Butman, TJ Kotz, CS Dowd- Frontiers in Cellular and, 2020 - ncbi.nlm.nih.gov | This review gathers literature reports on the structure /mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway... To date, there is very little information available for the Mtb PanE homologue (MtPanE). The activity of the protein expressed by the putative panE gene (Rv2573) has not been experimentally verified, although its crystal structure bound to NADP+ and oxamate has been solved (PDB ID: 4OL9). |
| 3 | 5b8i | - | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127630/ | Wen-Luo-Tong Decoction Attenuates Paclitaxel-Induced Peripheral Neuropathy by Regulating Linoleic Acid and Glycerophospholipid Metabolism Pathways | 2018 | F Wu, W Xu, B Deng, S Liu, C Deng, M Wu- Frontiers in, 2018 - ncbi.nlm.nih.gov | The structures of proteins were obtained from the Protein Data Bank ( PDB , https://www.rcsb.org/). Protein structures not available from PDB was homology modeled by (https://www.swissmodel. expasy.org) docking was carried out with Discovery Studio 3.5 (BIOVIA, USA) Table 6 Results of docking Proteins PDB ID pcat1 5b8i *Template of homology modeling. |
| 4 | 6nb3 | - | https://www.mdpi.com/1999-4915/13/8/1615 | What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2 | 2021 | V Fedorov, E Kholina, S Khruschev, I Kovalenko- Viruses, 2021 - mdpi.com | M-protein defines the shape of the viral envelope organizing CoVs assembly in the interaction with all other major structural proteins [9 Computational virology tools contribute greatly to the understanding of viral structure , infectivity and pathogenesis, and design of antiviral drugs ... The models of S-proteins of SARS-CoV and MERS-CoV were based on cryo-EM structures from the Protein Data Bank (PDB) with IDs 6NB3 and 5X58, respectively. |
| 5 | 3ujh | - | https://www.nature.com/articles/s41598-020-75650-0 | When a foreign gene meets its native counterpart: computational biophysics analysis of two PgiC loci in the grass Festuca ovina | 2020 | Y Li, S Mohanty, D Nilsson, B Hansson, K Mao- Scientific reports, 2020 - nature.com | F. ovina. Using simulated native-state ensembles, we examine the structural properties and binding tightness of the dimers. In addition, we investigate their ability to withstand dissociation when pulled by a force. Our results |
| 6 | 6n41 | - | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234869 | Whole-genome sequencing reveals origin and evolution of influenza A (H1N1) pdm09 viruses in Lincang, China, from 2014 to 2018 | 2020 | XN Zhao, HJ Zhang, D Li, JN Zhou, YY Chen, YH Sun- PloS one, 2020 - journals.plos.org | We searched and obtained the model template ( PDB ID: 6n41 .1.A) of HA protein of A/California/07/2009. We conducted a structure prediction of the trimeric HA protein by SWISS-MODEL, then the changes at the epitopes and RBSs were visualized in PyMol |
| 7 | 5upg | - | https://search.proquest.com/openview/c24741440c634a954b90086003c736d2/1?pq-origs... | Widening the Therapeutic Window: Time-Dependent Inhibitors of LpxC and InhA for Treating Multidrug-Resistant Bacterial Infections | 2018 | C Gu - 2018 - search.proquest.com | 46 Figure 2.10. X-ray crystal structure of paLpxC in complex with PF5081090 ( 5UPG . pdb ). ... 48 PD Pharmacodynamics PDB Protein Data Bank PIPES Piperazine-N,N-bis(2-ethanesulfonic acid) Sfp Phosphopantetheinyl transferase SKR Structure -kinetic relationship |
| 8 | 3mmt | - | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156105 | X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism | 2016 | LA Dadinova, EV Shtykova, PV Konarev, EV Rodina - PloS one, 2016 - journals.plos.org | ... When comparing the predicted structure of FbaB to ten of the closest structural analogs in the PDB, three fructose bisphosphate aldolase homologues were identified (PDB: 1OK6, 3MMT, 3BV4) along with four tagatose bisphosphate aldolases ... |
| 9 | 4v6h | - | http://scripts.iucr.org/cgi-bin/paper?dp5099 | X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp. strain AAC | 2017 | M Wilding, C Scott, TS Peat, J Newman - Section F: Structural , 2017 - scripts.iucr.org | ... After solving the structure, the difficulties associated with the molecular replacement from thehighly homologous sequence models became clearer, as despite their homology the structuresvary significantly. ... Similarly, PDB entry 4v6h (Seattle Structural Genomics Center ... |
| 10 | 3uam | - | http://core.kmi.open.ac.uk/download/pdf/11699007.pdf | X-ray structure and function studies of key enzymes for biomass conversion: GH6 cellobiohydrolases and GH61 lytic polysaccharide monooxygenases (LPMO) | 2013 | M Wu - 2013 - core.kmi.open.ac.uk | ... crassa Pch/P. chrysosporium Phanerochaete chrysosporium PDB Protein Data Bank PEG Polyethylene ... faecalis CBM33 (PDBcode 4A02)(Vaaje-Kolstad et al., 2012); PDB code 4ALC ... 4ALE, 4ALO, 4ALR, 4ALS, 4ALT) and Burkholderia pseudomallei CBM33 (PDBcode 3UAM). ... |