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 |
|---|---|---|
| 6Q04 | 2020 | 37 |
| 6NB7 | 2019 | 36 |
| 7K45 | 2020 | 33 |
| 7JZL | 2020 | 32 |
| 2LWK | 2012 | 32 |
| 3LAA | 2010 | 32 |
| 7JVC | 2021 | 29 |
| 7N8H | 2021 | 29 |
| 7JVA | 2021 | 28 |
| 6X79 | 2020 | 27 |
| # | PDB | Additional SSGCID structures cited | Link | Title | Year | Citation | Highlighted abstract |
|---|---|---|---|---|---|---|---|
| 1 | 6ptg | - | https://www.science.org/doi/abs/10.1126/sciadv.aea6832 | DksA inhibitors against intracellular and persistent Salmonella are effective in acute models of infection | 2026 | JS Kim, V Kumar, L Liu, YJ Choi, S Senovaityte- Science, 2026 - science.org | negative bacteria ( PDB 4IJJ and 6PTG ) were retrieved from the PDB database. PDB files were Schrdinger) programs to analyze the domain structures and amino acid interactions. The |
| 2 | 3gwc | 3hzg | https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6c01496 | The Impact of Second-Shell Residues on Substrate Binding at the Active Site of Thymidylate Synthase from Mycobacterium tuberculosis | 2026 | P Sengupta, P Satpati- The Journal of Physical Chemistry B, 2026 - ACS Publications | These structures indicate increased exposure of the active site between thermodynamics and structural characteristics ( to model the substrate-free MtbThyX, based on PDB 3HZG |
| 3 | 6mtz | - | https://www.nature.com/articles/s41586-024-08417-6 | Structures and mechanism of condensation in non-ribosomal peptide synthesis | 2025 | A Pistofidis, P Ma, Z Li, K Munro, KN Houk- Nature, 2025 - nature.com | the two parts with protein ligation 15, and solved the structures of the substrate-and product-bound states. The structures show the precise orientation of the megaenzyme preparing ... Initial phases were calculated by molecular replacement in Phaser v.2.9.0 using the full chain A (with domains F1A1T1C2A2T2) of Protein Data Bank (PDB) 6MTZ (ref. 14), followed by iterative refinement in the programs Phenix |
| 4 | 6tys | 6u1t | https://www.sciencedirect.com/science/article/pii/S1476927125000143 | Molecular modelling and optimization of a high-affinity nanobody targeting the nipah virus fusion protein through in silico site-directed mutagenesis | 2025 | NMO Odchimar, ANG Dulay, FL Orosco- Computational Biology and, 2025 - Elsevier | Nipah virus (NiV) is a re-emerging zoonotic pathogen with a high mortality rate and no effective treatments, prompting the search for new antiviral strategies. While conventional antiviral ... Protein datasets of experimentally described monoclonal antibody (mAb; PDB ID: 7K14) and fragment antigen-binding antibodies (FAbs; PDB ID: 6T3F, 6U1T, 6TYS, 7UOP, 7UPA, 7UPB, 7UPD, 7UPK, and 7UP9) in complex with NiV pre-fusion protein (NiVF) and NiV pre-fusion apoprotein (PDB ID: 5EVM) were retrieved from the Prot |
| 5 | 6tys | - | https://www.nature.com/articles/s41594-025-01598-2 | A nanobody-based therapeutic targeting Nipah virus limits viral escape | 2025 | A Isaacs, GV Nieto, X Zhang, N Modhiran- Nature Structural &, 2025 - nature.com | Data Bank ( PDB ) 5EVM) and other antibody-bound NiV F structures ( PDB 6TYS and 7UPD) to a previously determined cryo-EM structure of apo F ( PDB 8DNG), which faces inward |
| 6 | 6tys | 7ki6, 7ki4 | https://www.sciencedirect.com/science/article/pii/S016635422500141X | A monoclonal antibody targeting conserved regions of pre-fusion protein cross-neutralizes Nipah and Hendra virus variants | 2025 | T Li, H Xu, M Zhang, J Nie, B Liao, J Xie, Y Jiang, Y Liu- Antiviral Research, 2025 - Elsevier | The mAbs developed in this study and their conserved cross-neutralizing epitopes elucidated by structural analysis may contribute to the control of highly pathogenic HNV outbreaks. ... Local resolution estimation and filtering were performed using CryoSPARC. The cryo-EM structure of the NiV-F ectodomain (Protein Data Bank [PDB]: 6TYS) and crystal structure of the Fab (PDB: 7EJY) were aligned with the cryo-EM density map using UCSF Chimera |
| 7 | 7jzu | - | https://www.pnas.org/doi/abs/10.1073/pnas.2413465122 | Structure-guided engineering of a mutation-tolerant inhibitor peptide against variable SARS-CoV-2 spikes | 2025 | S Nakamura, Y Tanimura, R Nomura, H Suzuki- Proceedings of the, 2025 - pnas.org | The initial phase was determined by molecular replacement with Phaser (48) using the RBD structure ( PDB code 7JZU ) as the search template. The atomic model was rebuilt by manual |
| 8 | 6uhw | - | https://arxiv.org/abs/2507.14156 | All-atom inverse protein folding through discrete flow matching | 2025 | K Yi, K Jamali, SHW Scheres- arXiv preprint arXiv:2507.14156, 2025 - arxiv.org | structures for the sequences generated by both ADFLIP and LigandMPNN. We assessed structural similarity to the reference structure from the PDB scores from the structure prediction ( |
| 9 | 3o0m | 3oj7 | https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5273447 | Biochemical and Biophysical Characterization, and 3d Structure Modeling of Human Hint3, a Hydrolase of the Hit Superfamily | 2025 | R Dolot, M Sirerant, A Mikoajczyk- Available at SSRN - papers.ssrn.com | Structure modelling of the HINT3 (Gly36) variant revealed that the enzyme exists mainly in absent in the structures of HINT1 and HINT2. Analysis of the HINT3 structure shows that there... In a first attempt, a homology model for HINT3 was generated based on eight crystallographic structures with the PDB IDs: 5UVM, 6D6J, 6CVS, 3OJ7, 3O0M, 4INC, 3TW2, and 3O1Z (see Table S2) using the MODELLER 10.5 software. |
| 10 | 3fdz | 3gp5 | https://core.ac.uk/download/pdf/649473507.pdf | Revisiting the Plasmodium falciparum druggable genome using predicted structures | 2025 | K Godinez-Macias, D Chen, J Wallis- npj Drug Discovery, 2 (1), 2025 - core.ac.uk | To assess druggability evidence, we leveraged the AlphaFill database of predicted ligandtransplants based on homology of AlphaFold structures to all structures in the PDB REDO |