SSGCID
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 7n8i - https://www.nature.com/articles/s41592-022-01645-6 Improved AlphaFold modeling with implicit experimental information 2022 TC Terwilliger, BK Poon, PV Afonine, CJ Schlicksup- Nature, 2022 - nature.com To emulate the situation where no similar structure is present in the PDB , templates from the PDB were not used. For each protein we then examined the four AlphaFold models
2 7k43 7k4n https://www.nature.com/articles/s41401-021-00851-w 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 - nature.com 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);
3 2lwk - https://portal.ichb.pl/wp-content/uploads/2023/02/Doktorat_AleksandraJarmoowicz.... Small molecules interacting with Influenza virus RNA and SARS-CoV-2 RNA as potential inhibitors of replication 2022 A Jarmoowicz - portal.ichb.pl M121 structural motif of segment 5 (+)RNA secondary structure was investigated by importance of the conserved secondary structure of mentioned structural motif and suggest that it
4 7lxy - https://www.nature.com/articles/s41467-022-32262-8 SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization 2022 D Mannar, JW Saville, Z Sun, X Zhu, MM Marti- Nature, 2022 - nature.com structure , ACE2 affinity, and evasion of antibodies afforded by previously emerged variant spikes, providing a general structural coordinates ( PDB code 7MJG, 7MJM, 7MJN, 7LXY , 7K43
5 7jw0 - https://www.nature.com/articles/s41586-022-04980-y BA. 2.12. 1, BA. 4 and BA. 5 escape antibodies elicited by Omicron infection 2022 Y Cao, A Yisimayi, F Jian, W Song, T Xiao, L Wang- Nature, 2022 - nature.com Here, coupled with structural comparisons of the spike proteins, we show that BA.2.12.1, BA.4 and BA.5 (BA.4 and BA.5 are hereafter referred collectively to as BA.4/BA.5) exhibit similar ... b, Epitope of representative antibodies in group E3 (S2H97, PDB: 7M7W) and F1 (S304, PDB: 7JW0). Residues highlighted in red indicate mutated sites in Omicron variants.
6 7jv2 7jvc, 7jw0, 7ra8, 7ral https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010260 Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants 2022 A Mittal, A Khattri, V Verma- PLoS Pathogens, 2022 - journals.plos.org 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 6n41 - https://bibliotecadigital.exactas.uba.ar/download/tesis/tesis_n7210_SosaHolt.pdf Diseo, desarrollo y caracterizacin bioqumica y funcional de nanoanticuerpos VHH monovalentes dirigidos contra las protenas del virus de influenza tipo A 2022 CSS Holt - bibliotecadigital.exactas.uba.ar El virus de la Influenza tipo A contina siendo responsable de brotes y epidemias, adems de pandemias con graves consecuencias para la salud humana. Los virus tipo H1N1 y ... En ambos casos el templado con mayor posición en ranking fue el PDB 6N41(A/Netherlands/002P1/1951 (H1N1)) dado su alta identidad de secuencia
8 6wpt 7jw0, 7jx3 https://www.nature.com/articles/s41467-022-32665-7 Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape 2022 Z Zhao, J Zhou, M Tian, M Huang, S Liu, Y Xie- Nature, 2022 - nature.com targeted by S309 in the prototype (yellow) ( PDB : 6WPT ) 6 and Omicron (orange). Key ( PDB : 7JW0) 24 was aligned with our Omicron RBD-S304 structure and these two structures were
9 7jwk 6mu0 https://www.sciencedirect.com/science/article/pii/S002228362100588X Building structural models of a whole mycoplasma cell 2022 M Maritan, L Autin, J Karr, MW Covert, AJ Olson- Journal of molecular, 2022 - Elsevier PDB structure for a specific ingredient. Proteins with high sequence similarity and structural ... Ten of these experimental structures were used in our spatial model for the following gene products: MG396 (RpiB, 6MU0), MG027 (NusB, 1Q8C), MG191 .... The other four genes are only partially captured by experimentally-determined structures: MG200 (DnaJ-like, 4DCZ), MG238 (tig, 1HXV), MG301 (GapA, 7JWK), and MG469 (DnaA, 2JMP).
10 7ly3 7ral https://www.cell.com/cell-reports/pdf/S2211-1247(22)00798-7.pdf Cryo-EM structures of SARS-CoV-2 Omicron BA. 2 spike 2022 V Stalls, J Lindenberger, SMC Gobeil, R Henderson- Cell Reports, 2022 - cell.com The structures used in this analysis included PDB IDs 7KE8 (G6141), 7KE6 (G6142), 7KE7 (G6143), 7KE4 (G6144), 7LWS (Alpha), 7LYL (Beta), 8CSA (TM), 7LWL (Mk1), 7LWI (Mk2),