Seattle Structural Genomics Center for Infectious Disease

Cited Structures: list of articles citing SSGCID structures

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.

Cited structures

Manually reviewed citations

# PDB Additional SSGCID structures cited Link Title Year Citation Highlighted abstract
1 3h7f - Phylogenetic framework and molecular signatures for the main clades of the phylum actinobacteria 2012 B Gao, RS Gupta - Microbiology and Molecular Biology Reviews, 2012 - Am Soc Microbiol ...Structures of the S-adenosyl-l-homocysteine hydrolase (PDB accession number 3CE6) (240) (A and B) and serine hydroxymethyltransferase (PDB accession number 3H7F) (C and D) proteins from M. tuberculosis showing the locations in protein structures of the 9-aa and 5-aa actinobacterium-specific inserts that are found in these proteins...
2 7r7n - Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain 2022 G Ye, B Liu, F Li- Nature communications, 2022 - The atomic models generated in this study have been deposited into the PDB with accession number 7TGW (omicron open spike), 7TGX (prototypic open spike), and 7TGY (prototypic ... Forty-nine PDBs of neutralizing antibody/RBD complexes were analyzed using PDBePISA ... 7r7n, 7sn2. Fab: antigen-binding fragment.
3 6wps 7jw0, 7k45, 7jx3, 7jv6, 7jva, 7jvc Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies 2021 J Chen, K Gao, R Wang, GW Wei- Chemical science, 2021 - Our predictions are built from the X-ray crystal structure of SARS-CoV-2 S protein and ACE2 ( PDB 6M0J), 57 and various antibodies (PDBs 6WPS , 66 6XC2, 58 6XC3, 58 6XC4, 58 6XC7, 58 6XE1, 64 6XEY, 83 6XKP, 72 6XKQ, 72.
4 3uam - Structural Basis for Substrate Targeting and Catalysis by Fungal Polysaccharide Monooxygenases 2012 X Li, WT Beeson, CM Phillips, MA Marletta, JHD Cate - Structure, 2012 - Elsevier ... database (Protein Data Bank [PDB]) contains crystal structures of three CBM33 members, including S. marcescens CBP21 (PDB entry 2BEM) (Vaaje-Kolstad et al., 2005) and two other CBM33s (from Burkholderia pseudomallei and Vibrio cholera, PDB entries 3UAM and 2XWX ...
5 5unb - Assessment of hard target modeling in CASP12 reveals an emerging role of alignmentbased contact prediction methods 2018 LA Abriata, GE Tam, B Monastyrskyy- Proteins: Structure, 2018 - Wiley Online Library T0878-D1, 18.30, 12.84, 25.44, 344, 0.85, Burkholderia thailandensis, 5unb Panel E shows the structure of the full target T0912, rainbow-colored to highlight the discontinuities of its Target T0866 ( PDB 5uw2, a homohexamer, Figure 2A) was assessed as 1 evaluation unit of the FM
6 7jv2 7jvc, 7jw0, 7ra8, 7ral Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants 2022 A Mittal, A Khattri, V Verma- PLoS Pathogens, 2022 - Recent structural and functional studies have mapped the -CoV-2 variants; (2) the structural basis for antibody-mediated fitness, and in conjunction with the structures of the spike-nAb ... the neutralization mechanism involves direct competition with the ACE2 receptor. These antibodies include C002 (PDB: 7K8S) [70], C104 (PDB: 7K8U) [70], S2H13 (PDB: 7JV2) [77], C119 (PDB: 7K8U) [70], C121 (PDB: 7K8X) [70], LY-CoV555 (PDB: 7KMG), DH1041 (7LAA), COVA2-15 (EMD-22061) [82], 2–43 (EMD-22275) [94],
7 3p0x - Lifting the lid on GPCRs: the role of extracellular loops 2012 M Wheatley, D Wootten, MT Conner… - British journal of …, 2012 - Wiley Online Library ... Family A GPCRs: ECL structural aspects. ... 2RH1); B, D3R (yellow; PDB accession 3PBL); C, A2A R (orange; PDB accession 2YDO); D, CXCR4 (green; PDB accession 3OE0). ... In contrast, theECL2 of the β 2 AR possess a radically different structure comprising a short α-helix that ...
8 3dmp - Independent SE (3)-Equivariant Models for End-to-End Rigid Protein Docking 2021 OE Ganea, X Huang, C Bunne, Y Bian- arXiv preprint arXiv, 2021 - the 3D structure of a protein-protein complex from the individual unbound structures , of the initial locations and orientations of the two structures . Our model, named EQUIDOCK,
9 6nb7 6nb8, 6wps, 6wpt, 6ws6 Structural basis of SARS-CoV-2 and SARS-CoVantibody interactions 2020 E Gavor, YK Choong, SY Er, H Sivaraman- Trends in, 2020 - Elsevier While the binding of COV21 to the S-glycoprotein resembles the binding of the SARS-CoV S230( PDB : 6NB7 )[73], the binding interface SARS-CoV-2-S-S309-Fab[12] complex ( PDB : 6WPS/6WPT/6WS6) and the crystal structure of SARS
10 7k43 7k4n Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19 2022 C Wu, W Yin, Y Jiang, HE Xu- Acta Pharmacologica Sinica, 2022 - on uncovering structures and functions for structural biology of SARS-CoV-2 and discuss important biological issues that remain to be addressed. We present the examples of structure - ... S2E12 (represented as a cyan surface) binds to the “up” conformation of SARS-CoV-2 S RBD (PDB: 7K4N); S2M11 (represented as a brown surface) binds to the “down” conformation of SARS-CoV-2 S RBD (PDB: 7K43);