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 |
|---|---|---|
| 4EQY | 2012 | 11 |
| 4EO9 | 2012 | 6 |
| 4EMD | 2012 | 2 |
| 4EMB | 2012 | 2 |
| 4EM8 | 2012 | 3 |
| 4EM6 | 2012 | 1 |
| 4EK2 | 2012 | 2 |
| 4EGQ | 2012 | 2 |
| 4EGJ | 2012 | 1 |
| 4EGF | 2012 | 3 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 3men | - | http://pubs.acs.org/doi/abs/10.1021/bi101859k | Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases | 2011 | PM Lombardi, HD Angell, DA Whittington, EF Flynn? - Biochemistry, 2011 - ACS Publications | The recently solved X-ray crystal structure of the Burkholderia pseudomallei APAH dimer (PDB ID: 3MEN; 34% sequence identity with M. ramosa APAH) contains a 16-residue L2 loop insertion (A79−R101) between helices B2 and B3. |
| 2 | 3men | - | https://link.springer.com/protocol/10.1007/978-1-4939-8630-9_24 | Design of Drugs by Filtering Through ADMET, Physicochemical and Ligand-Target Flexibility Properties | 2018 | M Martnez-Archundia, M Bello, J Correa-Basurto- Rational Drug Design, 2018 - Springer | the three-dimensional model of the human HDAC6, considering some of the crystal structures available for this protein, which maintained some structural identities (2VCG (37%), 1ZZ0 (37%), 1C3P (29%), 3MEN (36%), 3COY 4. Finally, the crystal structure of PDB : 3F07 was |
| 3 | 3men | - | http://www.ingentaconnect.com/content/ben/cpd/2013/00000019/00000004/art00003 | Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives | 2013 | F Andreoli, A Jorge Moura Barbosa - Current , 2013 - ingentaconnect.com | ... Current Pharmaceutical Design, 2013, Vol. 19, No. 4 583 Table 1. Available 3D Structure ofHuman and Bacterial HDACs Class Name Organism PDB ID Ligand Domain Reference ... [262]Bacterial APAH Burkholderia pseudomallei 3MEN Catalytic Domain [263] a PDB ligand ID ... |
| 4 | 3men | - | https://www.degruyter.com/view/j/psr.2019.4.issue-10/psr-2019-0066/psr-2019-0066... | Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery | 2019 | V Chahal, S Nirwan, R Kakkar- Physical Sciences Reviews, 2019 - degruyter.com | Figure 2: Steps involved in homology modeling for 3D structure prediction sequences of proteins with known 3D structures available in various depositories such as PDB , using the In some cases, a single template is not enough to provide the complete structural information ... This catalytic domain was modeled using the I-TASSER server [98] by exploiting the solved crystal structures of some HDAC proteins having structural identities (2VCG (37%), 1ZZ0 (37%), 1C3P (29%), 3MEN (36%), 3COY (47%), |
| 5 | 3meb | 4otl, 4f4f | http://digitalcommons.unl.edu/chemistrydiss/86/ | Bioinformatic and Biophysical Analyses of Proteins | 2017 | J Catazaro - 2017 - digitalcommons.unl.edu | structure of every protein encoded within a particular genome, the aim is to concentrate to steadily produce structural representatives of previously uncharacterized genes. Although the new structures have been deposited in the Protein Data Bank ( PDB ) 4 |
| 6 | 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). ... |
| 7 | 3md7 | - | http://www.biomedcentral.com/1471-2148/11/273 | The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold | 2011 | F Fernandez, F Garces, M L?pez-Estepa? - BMC evolutionary biology, 2011 - biomedcentral.com | ... Furthermore, the recently determined structure of a MBL from Brucella melitensis subsp. abortus (PDB ID 3md7 and structures thereof) (unpublished) has revealed a monomeric enzyme with an Mn2+-dependent active site similar to UlaG and in contrast to the Zn2+ ligand found in all other RNases. . ... |
| 8 | 3md7 | - | http://pubs.acs.org/doi/abs/10.1021/bi2005398 | Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway | 2011 | SM He, M Wathier, K Podzelinska, M Wong? - Biochemistry, 2011 - ACS Publications | ... distances in angstroms. (d) Wall-eyed stereoview of the PhnP?orthovanadate complex superimposed with B. melitensis phosphodiesterase (PDB entry 3md7) bound to guanosine 5'-monophosphate (gray sticks). PhnP residues ... |
| 9 | 3md7 | 3r1i, 3oce, 3mx6, 3oca, 3r1j, 3o0m, 3r4t, 3r6f, 3omf | https://pubs.acs.org/doi/abs/10.1021/acs.jcim.6c00352 | Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy | 2026 | EH Snell, GW Grime, SM Webb, C Costa- Journal of Chemical, 2026 - ACS Publications | We find that in a majority of cases, the metals modeled in the corresponding PDB entries data integrity issue in deposited macromolecular structures , PDB -wide. These results establish |
| 10 | 3md7 | 3urr, 3uw3, 3swo, 3mqd | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257144/ | The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment | 2013 | S Chakraborty, R Venkatramani, BJ Rao… - …, 2013 - ncbi.nlm.nih.gov | ... PDB, NRes, NStructures, Specificity. ... based on the 'sequence to structure to function' paradigmis contingent upon the availability of its 3D-structure. The rapidly developing field of nextgeneration sequencing has exacerbated the bottleneck of obtaining structural data using ... |