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 | 3jvh | 3u04, 3ke1, 3k14, 3ikf | http://pubs.acs.org/doi/abs/10.1021/ci5004152 | Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function | 2014 | P Chaskar, V Zoete, UF Röhrig - Journal of chemical information …, 2014 - ACS Publications | ... Quality of the structure: resolution <2.5 Å, DPI <0.5 Å, ligand without missing atoms and ... of theligands, we extracted the respective coordinates from the Protein Databank (PDB) file, added ...Protonation states were determined based on pK a values and structural data for some ... |
| 2 | 3kre | - | http://pubs.acs.org/doi/abs/10.1021/ci400306m | Molecular dynamics perspective on the protein thermal stability: A case study using SAICAR synthetase | 2013 | K Manjunath, K Sekar - Journal of chemical information and modeling, 2013 - ACS Publications | ... PDB. The structure of SAICAR synthetase from E. coli (PDB-id: 2gqr), E. chaffeensis (PDB-id: 3kre), G. kaustophilus (PDB- id: 2ywv), M. jannaschii (PDB-id: 2z02) and P. horikoshii (PDB-id: 3u55) were considered for simulation ... |
| 3 | 3k14 | - | http://pubs.acs.org/doi/abs/10.1021/ci400020a | An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Programs | 2013 | I Giangreco, DA Cosgrove? - Journal of chemical information and modeling, 2013 - ACS Publications | ... All such algorithms must be validated with respect to known ligand overlays, usually by extracting ligand overlay sets from the Protein Data Bank (PDB). ... This is almost always done by reference to structures drawn from the Protein Data Bank (PDB). ... |
| 4 | 3kjr | - | http://pubs.acs.org/doi/abs/10.1021/ci300349s | Are homology models sufficiently good for free-energy simulations? | 2012 | S Genheden - Journal of chemical information and modeling, 2012 - ACS Publications | ... factor IXa (pdb code: 1rfn(36)) with 44% sequence identity and protein C (pdb code: 1aut ... Suitable template proteins for dhfr were found by a FASTA search(38) of the protein databank. ... The results of the FASTA search are summarized in Table 1. Finally, 2bl9, 3kjr, and 2oip were ... |
| 5 | 3k2h | - | http://pubs.acs.org/doi/abs/10.1021/ci300196g | Structural insights into the molecular basis of the ligand promiscuity | 2012 | N Sturm, J D?saphy, RJ Quinn, D Rognan? - Journal of Chemical Information and Modeling, 2012 - ACS Publications | ... To this purpose, we exploited the information in the Protein Data Bank (PDB)19 to identify ligands involved in complexes with different proteins. ... MATERIALS AND METHODS Identification in the sc-PDB of promiscuous ligands and their targets ... |
| 6 | 3glq | - | http://pubs.acs.org/doi/abs/10.1021/ci2005912 | Functional Prediction of Binding Pockets | 2012 | M Kontoyianni, CB Rosnick - Journal of chemical information and modeling, 2012 - ACS Publications | ... The dataset was compiled using the protein databank, the Structural Classification of Proteins (SCOP),68 the Enzyme Classification (EC)69 system and the Washington University Basic Local Alignment Search Tool Version 2.0 (WU- ... |
| 7 | 3pm6 | - | http://pubs.acs.org/doi/abs/10.1021/bi501141t | Structural and Functional Characterization of Methicillin-Resistant Staphylococcus aureus's Class IIb Fructose 1, 6-Bisphosphate Aldolase | 2014 | GC Capodagli, SA Lee, KJ Boehm, KM Brady… - Biochemistry, 2014 - ACS Publications | ... Using SaFBA along with the recent deposition of class IIb FBAs from B. anthracis (PDB Code: 3Q94) and Coccoidioides immitis (PDB Code: 3PM6) into the PDB, an updated categorization of class IIb subtypes can be envisioned (Figure 6) ... |
| 8 | 3md7 | - | http://pubs.acs.org/doi/abs/10.1021/bi500406h | Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cAMP and cGMP | 2014 | Y Tian, W Cui, M Huang, H Robinson, Y Wan - Biochemistry, 2014 - ACS Publications | ... structure. The atomic model was built with O(39) and refined with REFMAC.(40). The yPDE1 structure was compared with structures in the Protein Data Bank by the online program Dali (http://www.ebi.ac.uk/Tools/structure/dalilite). ... |
| 9 | 3uam | - | http://pubs.acs.org/doi/abs/10.1021/bi5000433 | Comparative study of two chitin-active and two cellulose-active AA10-type lytic polysaccharide monooxygenases | 2014 | Z Forsberg, ?K R?hr, S Mekasha, KK Andersson? - Biochemistry, 2014 - ACS Publications | ... Structural Sequence Alignment PyMod(27) was used to make a structure-based sequence alignment(28) of five AA10-type LPMOs with known structures: EfAA10A (PDB entry 4A02), BpAA10A (PDB entry 3UAM), VcAA10B (PDB entry 2XWX), BaAA10A (PDB entry 2YOX), and ... |
| 10 | 3swo | - | http://pubs.acs.org/doi/abs/10.1021/bi4003452 | Functional anatomy of complement factor H | 2013 | E Makou, AP Herbert, PN Barlow - Biochemistry, 2013 - ACS Publications | ... Three-dimensional structures have been determined, in the settings of FH truncation fragments,for ... Low-resolution structural techniques were used to investigate intact FH (discussed below)and several FH fragments,(39, 42-45) but no three-dimensional structure of full ... |